If you want to get some of the dust and debris out of your ventilation system, you can mix household cleaners like bleach with water, dip a cloth in the mix and then the wipe out the system. This will remove a layer of the spores, which could increase the quality of air a bit and help with the flow of air throughout the house until a pro can come out.
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.

Sounds like your first hvac company was ripping you off. Ask your new company to go to your coil and see if there is a leak. If there isn't the last company was just lining their pockets. If you have had ducts unhooked for a long time I would recommend duct cleaning, trust me I'm not a fan of duct cleaning myself. I have done hvac for 20 yrs. in GA. When I just bought a home built in 1996, we had all the ducts replaced immediately.
I even asked if this is something they don't do, as in services on a Saturday night.  I was told by the receptionist that they do and I would just be ok calling another company if they is not  part of their services. They again assured me someone WILL call me in 10 mins.  Well, unless their definition of 10 mins is never, then they got it wrong as I am still waiting to be called 5 days later.
My Carrier furnace occasionally (one-two times a day) does not start. It shows error code 15 ("BLOWER MOTOR LOCKOUT -This status code indicates the blower failed to reach 250 RPM or the blower failed to communicate to the variable speed furnace control within 30 seconds after being turned ON in two successive heating cycles."). However, when I turn off and on the furnace power switch it starts and runs fine for a while. Sometimes it runs fine all day, but does not start only once in the evening or in the night. It is 13 years old I was thinking to replace whole thing if repair cost is too high. But I am not ready to pay $10,000. 

As a homeowner and an owner of rental property I can tell you that the air ducts sometimes need to be cleaned. If you have had pets or anyone smoking in your home (even a visitor) for any length of time, having the ducts cleaned is really good idea. I had a tenant who did not smoke, but got married to a smoker more than year after moving in. When I realized someone was smoking I had them move out, but the smell was awful. I had the ducts cleaned and sanitized (it was a bit extra). The ducts were shiny like new afterwards. I left the windows open for a few days and we cleaned the place super clean and then replaced the carpets. The duct cleaning was worth every penny because the house looked, smelled, and felt new afterward. I plan to have my own house ducts cleaned again this year as we have two cats. We had them cleaned about 12 years ago and they found building materials in the ducts! If you move into a house that has never had them cleaned, it is good to do it. If you have allergies, clean the ducts to see if it helps. You never know what is in your ducts if you have never had them cleaned.

PickHVAC Tips: Electricity resistance heat is the most expensive heating type. You don’t want one of these unless you’re heating less than 30 days per year. The upfront cost of an electric furnace is much lower than the cost of a gas furnace. However, operating costs are two to three times higher. If winters are cold where you live, you’ll waste your upfront cost savings in just a few years of high electric bills.
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Although i love to burn candles, depending on the type your asking for problems big ones! At work one day i had been talking with co workers about these black shadows that were appearing on my ceilings and higher wall areas. They seemed to in the corners and along the stud supports , i could even see what i thought to be where all had been nailed. There would be dark shadows perfectly straight across my ceiling and then real dark circels every few inches within the lines. I thought it was the propane heat but learned quickly that oil heat will do that but not normally propane. A co worker brought me a magazine with a huge article about candles and what actually burns off them when lit, an ashy soot that is attracted to the areas on walls and ceilings that omit the most heat or warmth, of course where the drywall and studs meet and corners of the room. Its been about 8 years since i painted the entire house. I started bending to my love for candles again in the last 3 years, surprise i will be spending part of my summer re painting again!! No more candles ,well maybe at the holidays LOL
BIG THANK YOU for being honest, and advising us that for some reason the fuse/switch was in the reverse position so the AC unit would not properly turn on.   The unit turned back on immediately, and began cooling the house.   And then providing advice that the AC/Heating system needed some TLC, and giving us options to save money by purchasing a maintenance plan that included the filters plus cleaning services since we were already being charged for the service today.
In most modern homes with up-to-date heating and air conditioning systems, filters are changed regularly through the year, so you may not even need to hire a professional. However, keep your eyes open for the accumulation of dust, dirt, dander and mold. If you see it despite regularly changing your filters it could be an indication you need a high-pressure cleaning.
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?
Good article, but it fails to point out that leaky return-side ducts could be drawing dust and allergens into the duct system from the enclosed spaces in which they run, e.g. between walls, below floors, attic. So duct cleaning may only be a temporary solution. The homeowner can get a home energy audit -- free in many states -- to determine if they have significant duct leakage. An Aeroseal dealer may be able to effectively seal up the duct system without needing to tear into walls etc to get to the ducts.
Simply living in your home creates dust and dirt. Have you ever seen dust floating in the air in your home when the sun shines in?  Dust, dirt, pet dander, mold spores, and allergens get pulled into the air handling system in your home. They build up in the ductwork; some of it gets recirculated back into your home, and some of it can be captured by a good quality air filter. Eventually, enough debris builds up to the point where most of it blows back into your home. Your furnace or air conditioner must run longer to cool or heat your home, which costs you more in utility bills. With a service call from Sears Air Duct Cleaning, you can feel comfortable knowing that the accumulation of dust, dirt, dander, mold, and allergens has been cleaned from your HVAC duct system.
We were following up on this review and the service call we did for you. We could not find you in our system of ever having gone out to your home. If you could please provide us with the date we were out and the name under which the call was placed that would be great as we would like to see if there is any way we can rectify the situation. We do offer a 100% Satisfaction Guarantee, we have tried to private message you to no avail. Can you please call us at 925-318-4795?  
As one of the duct cleaners that do it right it disgusts me to hear the horror stories some of my past customers have had with the companies using scare tactics, bait and switch schemes, and just plain intimidation to make a fast buck. The Ductz franchise as a whole has gone behind other "duct cleaners" in the last year to the tune of almost three-quarters of a million dollars. All of this expense could have been avoided had the customers been able to do some background research before hiring. NADCA is a great organization and should be a minimum requirement for finding a duct cleaner. Other great questions include "How long does the service take?" (2 techs, 4-5 hours for a small house, 7-9+ hours for a two system house), "Do you clean the entire system including all trunk lines and the air handler (blower motor and evaporator coil)?", "How do you validate the job you have done?" (before and after picture reports work great). Beware of duct cleaners that say their process will solve all your air quality concerns. Duct cleaning is one of several steps to take to rid your home of unwanted dust, dirt, mold, and other allergens.

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