When you are saying it is clipping, which light is flashing red? If it is the comp light, I'm
pretty sure that shows input clip, not output
Have you replaced the valves?
Gear: Eden WT800B, 610xlt, 210xst (2) Sunn1200s, Berg NV412 Basses: Musicman SR5, Fender CS 64 Jazz, CS Reggie Hamilton V, MIJ '89 P bass, MIJ '94 Jazz Fretless, Ubass.