The short answer is yes, duct cleaning, done right by a reputable company will help with the smell. It is likely though the smell is coming from another source, ie the crawl space. It could also be that another rodent is dead in the duct work. A visual inspection would be in order to check for any breach in the duct system. A duct pressure test would be able to tell you how much air is leaking from the system over all. A hole large enough for an animal to enter would loses a great deal of air, over 300 CFM. It would be worth looking into having this test done and it should cost around $200. Cleaning the air handler and evaporator coil will greatly improve the performance of the air conditioner. Dirt and dust on the evaporator acts as insulation and reduces the amount of cooling done be the coil. Any quality duct cleaning should include cleaning the air handler and coil, and the tech should allow you to watch him perform the work as it is done.
The liquid refrigerant is returned to another heat exchanger where it is allowed to evaporate, hence the heat exchanger is often called an evaporating coil or evaporator. As the liquid refrigerant evaporates it absorbs energy (heat) from the inside air, returns to the compressor, and repeats the cycle. In the process, heat is absorbed from indoors and transferred outdoors, resulting in cooling of the building.
Consider what kind of heating and cooling system you want installed for the square footage of your home. Do you want a full system with a thermostat or a specific machine for the summer like a swamp cooler? Do you need a new furnace just for the winter? For any of these projects, the cost will vary depending on the quality, style and machine size you choose. If you have a tight budget, think of going smaller and upgrading over time. For example, if you can't afford to convert your entire home to solar power, you may want to consider only utilizing it to heat your water. Some other types of heating systems are:
My point is that the brand of equipment you choose is going to affect your HVAC installation cost greatly. People often call us for an air conditioning installation job and say, “I would like to install Carrier equipment.” Now, if you are a future client of ours, I’ll have to warn you – I can be a bit of a smart-ass. Why can’t work be fun? Besides…I was in the Navy for 11 years, what do you expect. 
EPA does not recommend that air ducts be cleaned except on an as-needed basis because of the continuing uncertainty about the benefits of duct cleaning under most circumstances. EPA does, however, recommend that if you have a fuel burning furnace, stove, or fireplace, they be inspected for proper functioning and serviced before each heating season to protect against carbon monoxide poisoning. Some research also suggests that cleaning dirty cooling coils, fans and heat exchangers can improve the efficiency of heating and cooling systems. However, little evidence exists to indicate that simply cleaning the duct system will increase your system's efficiency.

If you’re purchasing from a big-box store, you can expect to pay approximately $120-$1,000 for a window unit. Window units are appealing for their quick setup and relatively low cost, but they can use more energy over time than central air and only cool the room in which they’re installed. The price will vary depending on the type of air conditioner you buy and its cooling capacity. Window units, which require minimal installation, are one of the most affordable options on the market. Portable air conditioners don’t have the cooling power of a window unit, but they do have the perk of being transportable from room to room. Expect to pay between $225 and $800 for a portable air conditioner, on average. The cost of an air conditioning system with coils, condenser and line (not including installation or ductwork) can range from approximately $2,000 to $4,000 or more. If you don’t have (and don’t want to put in) ducts, a ductless mini-split air conditioner is a good option, although pricey up front. Pricing can range from $650 to $4,250 per unit on average; you’ll need one unit for each room in which you want temperature control.
Unfortunately, manufacturers and contractors don’t publish this information…it’s a secret. Why? Who knows…but we have access to a full contractor pricing database of 1,000’s of different units in our online HVAC installation cost calculator, so let’s choose one for our example calculation. We’ll go with Carrier equipment, since our readers always bother us about them (despite us telling them that they are overpriced):
The Environmental Protection Agency says that “duct cleaning services typically – but not always – range in cost from $450 to $1000 per heating and cooling system, depending on the services offered, the size of the system to be cleaned, system accessibility, climactic region, and level of contamination” and type of duct material. Consumers should beware of air duct cleaning companies that making sweeping claims about the health benefits of duct cleaning – such claims are unsubstantiated. Consumers should also beware of “blow-and-go” air duct cleaning companies. These companies often charge a nominal fee and do a poor job of cleaning the heating and cooling system. These companies may also persuade the consumer into unneeded services with and/or without their permission. (If you have knowledge of a practicing “blow-and-go” air duct cleaner, contact your local Better Business Bureau to report the company, and your local, federal, and state elected officials to demand legislation.)
Compressor -- Compressors are outdoor components in your system. The compressor is the pump that circulates the refrigerants through the air-conditioner. You can hear it when it's running so you'll know if it's working just by listening. If it starts getting louder, your compressor is about to fail. If it makes no sound when it should be on, it has already failed. Compressors fail for a number of reasons. Most often they fail due to strain from another failed part such as the fan motor. Electrical storms can also damage compressors. If the sound from the compressor gets louder or if you see a decrease in performance, you should have your compressor checked. A failed compressor will not heat or cool your house.
If you are replacing your air conditioning system, make sure that the unit is the proper size for your needs and that all ducts are sealed at the joints. A unit that is too big will cycle on and off frequently, resulting in poor moisture removal, particularly in areas with high humidity. Also make sure that your new system is designed to manage condensation effectively.
I always get a laugh at anyone claiming to be in the business for any length of time that doesnt understand the importance of cleaning out a ventilation system. Not only for better indoor air quality but for maintaining your heating equipment. I guess it makes more sense to some people that the furnace will just run better with a ton of dust and debris and maybe this wont be a big cause of sytem breakdown and malfunction. I mean really? Maybe this guy got a bad company and or cleaning and is a little jaded but to advise cleaning your grills , which does nothing, and replacing a filter....come on guy.
Outdoor Fan Motor -- The outdoor fan, also called the condenser fan, is exposed to external conditions. As such it is most prone to dust and debris and the extreme weather. In desert climates, the outdoor fan motor is subject to heat not only from normal operation but from the outside temperature as well. As it starts to fail, the fan may work fine in the cooler morning hours but stop by afternoon. This can shut down the entire system for hours. When they stop running completely, your air conditioner will no longer work. Running a faulty fan will lead to compressor failure, which is a very costly repair.
What about ringworm? If the fungus is as contagious as doctors warn, and the spores can live several months, doesn’t it make sense to spray some sort of fungus killer into the HVAC system to kill the spores that it has sucked in from the air? Duct cleaning would not be helpful at all here; these spores are microscopic and it could actually spread them further. But given how severely contagious ringworm is, body and especially scalp, does anyone make an aerosol product that will clean the system and kill the fungus? One the resident can use, not call an HVAC company; you can’t do that when you are in an apartment. I hear it’s not the same as mold, it is much more difficult. Truth?
Asking how much an HVAC installation costs is kind of like asking, “how much does a new car cost?”  Well, are you buying a Porsche or a Honda? Is it a 911 or just a Boxster, and are you going to get the leather seats? Likewise, are you going to get a Carrier or a Goodman air conditioner? Does the ductwork need to be replaced? These are all questions that will affect your HVAC installation cost, so let’s take a closer look.
Your HVAC unit and air ducts deliver heated or cooled air throughout your home year-in and year-out. The air your HVAC unit produces travels through your ductwork and heats or cools your home via the air vents in each room. The dust and other particles in your home’s air are known as particulate matter, which the EPA defines as "a complex mixture of extremely small particles and liquid droplets." The EPA also notes that "particle pollution is made up of a number of components, including acids (such as nitrates and sulfates), organic chemicals, metals, and soil or dust particles." Having clean air ducts means fewer of these particles moving through your home. If you remove your furnace filter and hold it up to the light, you can probably see several hundred of these minuscule particles floating in the air. 
If you are using existing ducting, it will have to be inspected. Proper ducting loses around 2% to 5% of your energy. Old, leaking ducts can lose 50% or more. A contractor will need to have the ducts inspected and replace any parts ahead of time. If you are changing the size of your HVAC system because of significant changes to your home, you might need to replace the ductwork regardless.

Here in Frisco, TX…just had a tech come out to clean vents. I used a 30 bucks groupon for “complete vent cleaning”. He told me I have 3 AC units and groupon covers only 1. I told him to do the unit upstairs where the kids sleep. He decided on his own to do the downstairs unit. I yelled at him why he is not doing the unit I told him to do! He said they are all connected. I will clean two for you for the price of one… Oh really?
What you might not know is that the brand you choose is one of the most important factors in determining a fair HVAC installation cost. So, before delving in-depth, let’s take a quick look at the average prices of a new air conditioner and matching coil by brand…keep in mind, these are the average prices (by brand) that contractors pay for your AC equipment, and it is meant to give you a rough guideline until you are closer to buying:
A small number of products are currently registered by EPA specifically for use on the inside of bare sheet metal air ducts. A number of products are also registered for use as sanitizers on hard surfaces, which could include the interior of bare sheet metal ducts. While many such products may be used legally inside of unlined ducts if all label directions are followed, some of the directions on the label may be inappropriate for use in ducts. For example, if the directions indicate "rinse with water", the added moisture could stimulate mold growth.

Fresh-Aire UV is an innovation leader in the field of indoor air quality. Our award-winning UV light and carbon products fight mold, bacteria, viruses and odors in commercial and residential HVACR systems. Our products include Blue-Tube UV®, the worlds most popular germicidal UV light, the revolutionary APCO® PCO/carbon whole-house air purifier, and Mini UV the first UV light system designed specifically for mini-split AC systems.
"Customer service was great, and the price was in-line with other places, and fast service. We had a whole replacement of the outside and inside. I would have liked to see a better install for the furnace and new thermostat - the new thermostat should have gone where the old one was, and even tho the new furnace was a tight fit, they didn't offer to come back and repair the case molding, or give me a discount on the damage done, and I believe they should have put a disconnect box on the outside of the home, to make it easier for any future repairs needed. Other than that, am very happy with the cooling and heating!"
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