i am SO thrilled to see that damn thing running.
as far as clunking, yes i'd be willing to say an axle is bad. when my flex plate was changed, of course the axle was removed to lower the frame, and when the axle was disturbed, it went to chit. so since you disturbed it, i'd be willing to say it's bad. but that's just on personal experience.
best of luck, and please enjoy that damn thing.