Mitch,
From what you describe it seems like you've got a poor solder joint somewhere along the 30/20m LPF path.
So, a close visual inspection of the board around that area is a good place to start followed by a reflow of the PC-board's connections for that LPF.
Perhaps when you were moving the windings of that filter it was just enough to loosen an cold solder joint?
For isolating signal flow faults, I think it's better to use QDX's built-in diagnostics, AF sweeps, RF sweeps, TX-tests in a terminal session. But, they won't test the antenna connector or signal flow through C2.
You can also test cathode voltages on the switching diodes in a terminal session, too. Searching this forum should bring them up.
Good luck!!
--Al
WD4AH