one thing Ive learned about dialing in amps is, the controls on every amp are different and dont be afraid to think outside the box. It seems to me like youre trying to dial in your Boogie the same way Jerry dialed in his Twins pre-amp in order to cop some Jerry-like tones but that might not work because youre playing through a different amp altogether. I have never really spent much time with Boogies so I cant really help you but I would just try turning knobs all different ways and listening to the effects each one has rather than looking at numbers. Fenders have an abundance of Bass so thats why Jerry dialed his way down - which Im not sure is the case with Mesas.
Ive found my best lead tone with my pedal setup going into my Pro Reverb is with the Bass-3, Treble-3 and bright on, so go figure. Then again Im not playing in a Dead band.