DS1 Keeley mod issues

[bubish]

So I am doing the Ultra mod/All Seeing Eye mod to a DS1 (as described here: http://www.robertkeeley.com/audio6l6/dstech.html), and I running into a couple of weird issues.

The biggest problem is a rapid, rhythmic thumping noise whenever the distortion is turned up much beyond half. It goes away when I play a note, but will come back as the note decays.
The other things I noticed are the tone pot does not seem to affect the signal at all. Also, the pedal seems way hotter than it should (even with level and distortion all the way down, the pedal is still more than twice as loud as the unaffected signal.)
When I hit the bypass switch, the signal goes back to normal.

After staring at the thing for many hours (and some prodding with the multimeter), I've concluded that all the solder joints look solid, and I don't see any shorts. None of the components look fried either.

So far I have checked both the 9v and 4.5 volt positive voltages, and they are right on.
I also tried to isolate where in the circuit this noise starts, but when I probe the circuit, I still get the noise all the way back to the tip of the input jack! (Again, however, only when the effect is switched in.) When it's set to bypass and I probe the output of the opamp, the noise still does show up, though a little faster and a little quieter.

So to finish off this book of a post, I have no idea what's wrong or where to go from here.

Please help!

P.S. This is my 5th time doing this mod, and I've never had any issues with it before. In fact, this pedal is by far my cleanest looking job yet!