I would call someone that does professional cleaning after fires etc. and see if they can give you a suggestion. Might be you could put the customer in touch with these people as your job is done once the motor was replaced, unless you also provide remediation services.
Depending on what is in the duct work as far as dust or even duct liner, the smell may be hard to get rid of. The stuff (depending on it's makeup) can attach to most anything and stink for a long time.
Use the biggest hammer you like, pounding a square peg into a round hole does not equal a proper fit.