The way you described your sound with PF attached after the preamp ("trapped within a tiny box") makes me think that maybe you should check your Killdry setting in PF. If the effect loop section of your amp is marked as parallel, you should set Killdry to ON, to avoid phase problems caused by running two dry signals at the same time. If your efx loop is serial, you should set Killdry to OFF and than set the amount of processed (pitched) tone with dry/wet knob.
If Killdry setting doesn't solve a problem… I would suggest 3-amp-configuration. Your JCM could remain the main amp, and the other two (possibly smaller and cheaper) could monitor your stereo effects – choruses, delays, modulation, pitch, anything that comes after the preamp in your chain. In my honest opinion, that is the only way to keep your initial tone uncompromised, not only with PF but with any effect box on the market.
Hope this helps.