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.
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.

Duct cleaning has never been shown to actually prevent health problems. Neither do studies conclusively demonstrate that particle (e.g., dust) levels in homes increase because of dirty air ducts. This is because much of the dirt in air ducts adheres to duct surfaces and does not necessarily enter the living space. It is important to keep in mind that dirty air ducts are only one of many possible sources of particles that are present in homes. Pollutants that enter the home both from outdoors and indoor activities such as cooking, cleaning, smoking, or just moving around can cause greater exposure to contaminants than dirty air ducts. Moreover, there is no evidence that a light amount of household dust or other particulate matter in air ducts poses any risk to your health.
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