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.
These are the prices for a proper installation from a professional – as a word to the wise, HVAC systems require fine tuning and the custom fabrication of parts during installation to work properly, otherwise they will likely fail prematurely. But there are plenty of people who will do it for cheaper than this, using substandard, used, or stolen equipment (stolen from construction sites and new housing developments). Or, they are using unskilled laborers with no experience, etc. But HVAC is not a “we’ll figure it out trade;” there is a right way and a wrong way to do things. There are just too many predatory companies out there, so be careful. I’d highly recommend not skimping on your HVAC contractor. If you go cheap, you will typically pay more in the long run...and in California, that will be a lot!
They are also often harder to install. A proper location on the roof must be selected that can support the weight of the unit. Then a platform must be built and a drain pipe for the unit must be run along the roof to avoid problems with mold and corrosion. A crane must be used to lift the unit onto the roof while a team guides it into place and hooks it up.
Had our ducts cleaned late April, 2016. Sodium Chlorite was sprayed into ducts after cleaning. Ever since, we have been bothered with eye and nasal passage irritation because of a “chemical” and “musty” odor. This odor is present whether or not a/c is on.) We are told the sodium chlorite (“EnviroCon, manufactured by Bio-Cide International) is used in hospital and nursing home settings and is not hazardous to health. The air duct company’s suggestion is that they come out and spray even more sodium chlorite…we absolutely don’t want this done! Have had various other recommendations about what we need to have done to remedy our problem. We will be unable to stay in our home if a resolution cannot be found. We’d be willing to replace the ductwork if necessary. (One professional suggested that the cleaning may have “knocked something loose” inside the ductwork and that is the source of the irritant.) This home was built in 1920…no idea when the present ductwork was installed. Any suggestions would be appreciated.
In reading through all this about duct cleaning, THE ONE preventative measure people need to realize is that a poorly installed HVAC system that is not sealed and air tight to ensure that ALL indoor air passes through a GOOD air filtration system IS THE best means of ensuring your ducts remain clean. Duct cleaning does not now and will NEVER improve an HVAC systems efficiency. Proper maintenance and installation are the key just as improper installation practices allow for dust infiltration into the duct system. I am a state licensed contractor in Texas, and unless people have their hvac system sealed and/or properly installed, duct cleaning is an absolute waste of money. My duct system is 12 years old as is as clean today as the day I installed the system with ductwork. SO before ANYONE jumps on the bandwagon of duct cleaning, get with your hvac professional FIRST.
In addition, the service provider may propose applying chemical biocides, designed to kill microbiological contaminants, to the inside of the duct work and to other system components. Some service providers may also suggest applying chemical treatments (sealants or other encapsulants) to encapsulate or cover the inside surfaces of the air ducts and equipment housings because they believe it will control mold growth or prevent the release of dirt particles or fibers from ducts. These practices have yet to be fully researched and you should be fully informed before deciding to permit the use of biocides or chemical treatments in your air ducts. They should only be applied, if at all, after the system has been properly cleaned of all visible dust or debris.
Having the most energy-efficient system ever built won't matter much if it's not maintained. Lack of maintenance is the number one killer of HVAC systems. Before each cooling season, it's recommended that your system get a professional tune-up. However, there are things you can do in the meantime to make sure your system runs efficiently throughout the year.

An alternative to packaged systems is the use of separate indoor and outdoor coils in split systems. Split systems are preferred and widely used worldwide except in North America. In North America, split systems are most often seen in residential applications, but they are gaining popularity in small commercial buildings. The split systems are a great choice for small buildings where ductwork is not feasible or where the space conditioning efficiency is of prime concern [20]. The benefits of ductless air conditioning systems include easy installation, no ductwork, greater zonal control, flexibility of control and quiet operation [21]. In space conditioning, the duct losses can account for 30% of energy consumption [22]. The use of minisplit can result in energy savings in space conditioning as there are no losses associated with ducting.
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.
One of the difficulties encountered by many air duct cleaning service companies is that their attention is not really on air duct cleaning. For example, many heating and cooling companies offer duct cleaning as a supplemental service, but of course their primary business is installing and servicing heating and cooling equipment. For these companies, air duct cleaning is not always given the attention it deserves and is often done by less experienced employees whose interest is not in duct cleaning but in repairs and installs. And it is almost always done with inferior air duct cleaning equipment. Still other firms (like carpet cleaners) offer a large variety of services and claim to “do everything.” Because of their lack of focus they may not actually be very good at many, if any, of the services they offer. They cannot simply buy an attachment for their carpet cleaning machine and magically become a great duct cleaner.
Dehumidification (air drying) in an air conditioning system is provided by the evaporator. Since the evaporator operates at a temperature below the dew point, moisture in the air condenses on the evaporator coil tubes. This moisture is collected at the bottom of the evaporator in a pan and removed by piping to a central drain or onto the ground outside.

A Full Installation is the most common type of HVAC installation for a reputable contractor. The ductwork adds two days of labor and about $2,000 to $3,000 to the price, but realize that this is a very important part of your HVAC system. Although it might sound like a good idea to reduce HVAC installation cost and get a quick change-out, realize that there is dirt and debris collecting in your ducts, and the ducts themselves develop holes and full breaks over the lifetime of your unit, all of which may be hidden from sight by insulation. Remember, many contractors will push a quick change-out on you because it is easy and good money for them – you need to be involved and ask questions.

The most recognized standards for HVAC design are based on ASHRAE data. The most general of four volumes of the ASHRAE Handbook is Fundamentals; it includes heating and cooling calculations. Each volume of the ASHRAE Handbook is updated every four years. The design professional must consult ASHRAE data for the standards of design and care as the typical building codes provide little to no information on HVAC design practices; codes such as the UMC and IMC do include much detail on installation requirements, however. Other useful reference materials include items from SMACNA, ACGIH, and technical trade journals.
Duct cleaning generally refers to the cleaning of various heating and cooling system components of forced air systems, including the supply and return air ducts and registers, grilles and diffusers, heat exchangers heating and cooling coils, condensate drain pans (drip pans), fan motor and fan housing, and the air handling unit housing (See diagram).
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