Thanks for all the great advice recoder. I've got the game running pretty smoothly using the settings you recommended earlier on. For anyone else in this sort of situation, here's what's worked best for me (in terms of audio skipping and maintaining reasonable framerates in Tartarus and the classroom):

EE Cyclerate - 3
VU Cycle Stealing - 1
Four upper speedhacks (left out the boot CDVD or whatever.. the one that says not recommended)

When a boss fight is going to slow to tolerate, switch to Native res and you should get through it np.

The only glitches I've come across are:
1) sometimes PCSX2 will crash during a day changeover; i havent figure out what condition causes this yet. Usually requires a load from memory card to rectify (save often! save states aren't reliable imho)

2) When battling precisely TWO enemies that have revolving physical properties (i.e. tiaras, phantoms, twins, etc.), if i cast a spell from my MC against the default target, the game will hang... i can still hear music and animation continues, and i can switch to "Rush" by hitting triangle, but the camera stays in place and all progress reaches a halt. To get around this I will generally just hit "Wait" and use support spells until my party members have dispatched one or both of the baddies on their own.

Other than that its just been some audio flaws and some slowdowns, but a small price to pay when it mean playing P3FES again at last! thanks everyone!