Nice analysis - while we're waiting for Mr. Carlton to step in... you mention you've vac tested the modulator and it held. Did you also test the VCV (engine off) to see if it is holding vacuum, or how quickly it drops?

It would be interesting to have a guage in the car "t-ed" to the modulator line to see what amount of vacuum you're getting when you begin to press on the accelerator. Based upon previous reading, I associate clunking to mean too little vacuum..

__________________
83 300d - 390k