Hi Chris,
let me see if I can help you out here. rather than you get stressed. after all, this kind of work is my speciality. GPU flashing in most cases is rather intensive if you've not already tried this. certain cards require a 2 way flash procedure and this gets dirty. the reason is because OS X doesn't always support or identify a GPU that's not officially coded by apple and in doing so, limits the amount of available supported GPU's on the market to certain rather pricy high end units.
In flashing it's important to remember that you're going to need a windows PC with a compatible motherboard for the GPU in question. it's handy to have either an open board on a clean desk powered, etc ready for use or as certain engineers I know would use an external chassis with a bridge controller to a host. The software used requires flash rom files that have been recompiled to do so. from there, once the GPU's flashed, tested, then OS X has to understand what GPU this is and there's some programming / resource editing involved. SOMETIMES THIS DOES NOT WORK! so I must make this clear.
ProtoolsLE5Guy's links can be helpful to a degree but remember this. it's not only the GPU delivering the performance, it's the logic board as well. AGP slots etc are clocked at specific data rates so they don't overload the main host running channels and as such will support upto a certain performance card. OS X 10.4 also has a different layer for GPU control with openGL as well as it's other GPU callouts so remember, if the GPU in question performs perfectly in 10.3, it's because of an old version of openGL built in to OS X, quicktime support, etc. there are many variables that exist in this framework.
I've been researching this myself and I too admit to a senior moment or two lol.
I'll make this bit clear. My concern regarding GPU's bears relevance to the operation of screen readers which translate data to speech relying on stable GPU's A GPU in my case isn't for getting amazing graphics, I rely on high end GPU's to maximise the potential data translative threshold to achieve quicker results. this isn't just in having a screen reader speak what's on screen, but also in translating documents via OCR where the GPU is working to translate in tandem with CPU and logical code.
I too am in the throws of the argument of taking out the factory installed GPU in a G4 MDD 1.25 single customised from an 867 dual. my challenge is finding 1: a compatible AGP card, 2: a card capable of being flashed to support OS X / OS9 for better performance, so as not to take from mainboard RAM any further on generating various streams of data via a screen reader.
If I can help, message me your email off list and between us, I hope I could help you.
take care chris.
ed.