Without further ado, here are the mods, straight from Heath: 
anything said after "NOTE" is my addition or comments.

1. Change the coupling caps (c4, c5, c14) out for .0022uf caps. 
This will thicken up the preamp alot and get rid of the cocked 
wah sound. Also warms up the clean channel too.
The coupling cap(C14 .001uF) feeding v2a rolls off everything 
below 340hz, replacing this with 0.0022uf (aka 2200 pf) makes 
it roll off at around 150hz, restoring some bottom. 

Also the cathode bypass cap on V2a (C17 .47uF) is cutting below 
450hz. Replace that one with a 1.0 uF to move the cutoff 
frequency to 205hz. 
NOTE that heath said the C17 mod made the preamp borderline muddy, and he later reversed it back to stock.

2. The stock voltage the preamp tubes are seeing is 260v give or take. 
This is not the best sounding voltage for a preamp like this. 320 or 
so is much better. Change R33 and R34 out for 4.7k resistors. This 
will bring this preamp to life.
NOTE: I think he's referring to the plate voltage feeding the preamps. 
This will raise the current going through the tubes, and should cause
more grid-current-limiting which is what you get when you bias warmer. 

3. Change the plate resistors to 100k(R3 and R13 only) This will give 
less distortion but a rounder gain. 
NOTE: The stock resistors are 150k. Lowering this value causes higher 
grid current, similar to the above mod which sounds more "vintage" or 
"mellow" due to slightly more even-order-harmonics. Using a larger 
value here results in harder clipping and slightly more odd-order 
harmonics, which sounds more "aggressive" and "modern". The highest 
you should go is 200k, anymore and it will oscillate.

4. Replace the ultra gain pot with a 50k This will make it a clone 
of the crunch channel(I did the opposite and changed the crunch pot 
to a 1M...I am gain freak I guess). 

5. The Mid control on the clean channel EQ doesn't really work so 
well. As you turn it clockwise it adds more mid-bass, but keeps an 
overall scooped response. This is caused by a capacitor across the Mid 
potentiometer. Peavey used a .015uF cap (C9) there. You could simply 
remove it, but that will result in the mid pot turning into more of a 
gain control considering its 50k ohm value. Instead, I recommend 
replacing C9 with a smaller value, between .003uF to .005uF.

6. The effects send & main outputs' coupling caps are too small, and may 
act as a low cut filter. This is noticeable if the unit is plugged 
into products with an input impedence below 100K ohms. The result is a 
thin sound, which is especially noticeable on the clean channel. To 
prevent this replace C40 & C30 each with a 1uF 400V film cap. You may 
be able to get by with a 250V cap, it all depends on the cathode 
voltages at each location."


These are in no particular order, and have not been personally tested 
by me, so grain of salt is in order. However I do plan on doing all 
of these soon, so watch out for a post reviewing the mods, or an 
angry rant about how I fucked it all up.