sometimes it works when switched on for a few seconds but usually I just get a "thump" sound when I press a key. audio is making it to pin 3 on the lm13600 vcf. outputs on 8 and 9 seem extremely low.

There are trouble-shooting checks and tests including voltage measurements at the VCF and VCA section ICs 17 and 18 here:

viewforum.php?f=15

When built in the desktop enclosure, the board can spring against the case bottom and if it does this with power applied, it can damage IC 17 at the back corner where it's more likely for contact to occur. Putting stick-on rubber bumpers, taller than the joints, at the back corners of the board will work to keep the board pressed away from the bottom.

If you can send photos of the board soldering in the area and panel control wiring connections (VCF and VCA sections), I'll let you know if I see anything awry (email to scott@paia.com).