meh, i dunno man. that chassis has got to be crowded as fuck.
theres like 6-8 EQ's based on the old school inductive/capacitive layout which takes up alot of room, the power supply itself is complicated, theres alot going on in that section of the schematic and i can imagine the space its taking up. im not sure about the head version you found, but im guessing its not too far off from this.
then the preamp itself has a tonestack early on in the preamp, ala fender's older designs which would probably need to be moved, as tonestacks normally dont sound their best in that position when gain is concerned. that is a matter of opinion of course, but i would be considering moving it if it were me. i like a tonestack after cascaded high gain stages, not in the midst of them. you get better control the way it is in the schematic, but its just not the same.
if you like the clean tone id suggest keeping it as it is, and looking at another amplifier as a doner. because the more you fiddle with that one the more money you are going to tie into it. i mean if someone really had the time that has great potential to be a killer amplifier, but that chassis has got to be tight and noise would start to be a concern, so im sure the grounding layout of that amplifier would need to be updated as well to keep things minimal, i mean theres just alot of labor involved in it that is more than normal.
depends on how much you love the clean channel and how deep you want to go with it. i mean to be honest anything is possible, but the guys that mod them here on the board want amplifiers with the least amount of BS to make building their designs easier and more professional, and that fender has got alot going on that isnt completely normal - but not uncommon for its erra of course. i still say look elsewhere.