Air conditioning and refrigeration are provided through the removal of heat. Heat can be removed through radiation, convection, or conduction. Refrigeration conduction media such as water, air, ice, and chemicals are referred to as refrigerants. A refrigerant is employed either in a heat pump system in which a compressor is used to drive thermodynamic refrigeration cycle, or in a free cooling system which uses pumps to circulate a cool refrigerant (typically water or a glycol mix).
The EPA is so far behind on useful knowledge because of the lack of funding so don't be mislead. The Hvac old timers were left at the dock so to speak and missed out on the IAQ movement. The ones that are savvy and up to date on the information do Air Duct Cleaning, even tho that will lead to a few less service calls its the right thing to do for their customer. Please take a look into a return duct that has never been cleaned, I dare anyone to say it does not need to be cleaned.
R-22 Freon is being phased out & isn't readily available. So the service company may only purchase as needed and the lack of availability would make their cost high. But, as long as they can get it, whatever the cost, unfortunately, is less expensive than replacing the A/C. Which will be the case eventually since it's no longer manufactured or sooner as in my case with a not so old a/c that sprang a leak, that would have been just a repair, but since it uses R-22 the whole unit has to be upgraded(replaced).  
SEER is useful for comparing one model to another much in the same way that a car's calculate MPG is useful. It's not an accurate prediction of exactly how efficient the system is, but it can tell you which one is more efficient. Also, since SEER is based on a "cooling season", what region you live in will determine how long or short your cooling season is.
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.
Wiring up the thermostat is usually pretty straightforward if an old one is being replaced. If a thermostat is being put in where one had never been before, that could involve running new wiring. The placement of the thermostat is also important so that its sensors can get an accurate reading of the temperature. A thermostat that is blocked by a bookcase or other large furniture will not get a good reading and will not perform efficiently.

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.
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