possibly bad motor mounts
sounds like they are going bad and your exhaust might be hitting the floorboard? does the car have aftermarket exhaust. and glad you went with poly tranny mouns those help out alot, now u might need to do poly engine mounts so you dont have to do either one again. also the clunk could be the torque arm mount neat the tranny as well.
If that seems fine, and you still think they are bad, get it up on stands and just have a look at the rubber. Is it cracked/brittle/worn looking? It might not be broken but it can still be worn out.

