I seem to recall that the set screw on the bottom of the amplifier will reduce vacuum when turned fully clockwise..........but........I haven't adjusted it in awhile.

In any case, try the amplifer with the set screw fully counter-clockwise. It takes a 4mm socket........which you probably already realize.

Also, try a test with just the Mityvac connected to the modulator. Pump up the Mityvac to 15" and leave it there. Take the vehicle for a test drive and see how it does. If the vacuum falls during the test, pump it back up to 15". See if the clunk disappears.