Read the thread, PlaneSailing, and agree with what you're saying with regards to simplifying the game. I don't want to mess with the mechanics of stacking bonuses, per se, but rather, from a game management stance , make it easier on everyone.
To cope with running spells now we have both an initiative scribe (the alternate DM) and a big dry erase board behind the DM with all the PCs names followed by any spells, potions, ability loss, et cetera acting upon them. It works, but it (as you well know) can be a real pain in the ass.
Hmmm.... will wait and see what other replies show up and go from there I suppose.