I live in a 1950's ranch house in the South. The prior owners were smokers. Based on recommendations from one of the local conservation organizations, I decided to have a home energy audit done. As part of their findings, they recommended additional insulation in the attic and duct cleaning and sealing. This turned out to be a very problematic process. In terms of the ducts, it was necessary to remove the metal grates. However, these grates had been painted over many times and shoe molding covered the bottom of the grates. The vendor was not able to remove the grates without damaging them in the process. Because these grates dated back to the 1950's, it was difficult to find appropriate replacements. The ones I finally discovered were correct except they were 1/4" wider. This meant that the shoe molding had to be carved out. The duct cleaner could not provide any assistance with this problem. It took me a month of long evenings replacing the vent covers myself, carefully chiseling out the shoe molding and repainting. In terms of the extra installation in the attic, the same vendor used blow in insulation. Unfortunately, they did not recognize that the 13 floodlights whose mounting extended into the attic were not designed to be buried under insulation. The problem manifested itself in terms of expensive flood light bulbs failing continually. So, I had to have all of the light housings replaced. Yet another unexpected expense. Despite the expense, pain and suffering, I cannot report any improvement in my heating costs or the "quality" of the air. To be fair, I do not have any allergies and did not undertake this for air quality improvements but rather heating efficiency improvements.
The amount of debris or mold present in your system could certainly ratchet up the overall price. The cost of mildew removal is around $0.07-0.08 per square foot, on top of your initial cost, according to Blue Book. Removing these elements involves added time, special equipment and even special chemicals. In fact, you may be referred to a specialist if mildew and mold is too severe.
You should be aware that although a substance may look like mold, a positive determination of whether it is mold or not can be made only by an expert and may require laboratory analysis for final confirmation. For about $50, some microbiology laboratories can tell you whether a sample sent to them on a clear strip of sticky household tape is mold or simply a substance that resembles it.