I've hit the same problem. Using an Aguilar OBP3 preamp. Now my fuzz pedal sounds like trash, though my cleans sound great!
Looks like I'll have to house the preamp, and put it after the fuzz. Not great for making tone adjustments on the fly!
Another way to get some extra top end - change the pot value to 1 meg. I've done it to a few instruments, and it really works.
Also physically small pots don't sound any different to big pots, as long as they're reasonable quality. They're just trickier to solder on the back without damaging