Yeah I've had problems with some PCI cards not working at all. I have some cheap USB 2.0 PCI cards that refuse to show up at all in this board (sometimes won't power on at all). The problem with these old chipsets is that they only have 15 IRQs (today we have APIC and many more IRQs) and the PCI bus only has 4 to go around. So sharing is inevitable, but that's not usually a big issue unless the cards/drivers are very poor or the board isn't the best. So I blame 1) old OS's 2) Abit's board quality 3) Intel's chipset limits. By the way, XP is better than 98SE at managing IRQ sharing.
Running 3 DIMMs increases the load on the memory controller. It's the same with modern systems. More DIMMs means that the signal isn't as strong, more electrical noise, etc. This is the reason that Abit set the 3.3v I/O voltage to 3.5v instead, by default. More volts gives a better signal. RAM latencies almost always have to go up with 3 DIMMs.
And about the capacitors, I actually replaced all of mine with a set from badcaps.net (or whatever it is). I had a few that were bursting and even though the board was working alright I figured it would be a fun little diversion to replace them. It's not a trivial task though, desoldering all of those old caps. The board doesn't really work better now than before either so I guess a few bad caps isn't the end of the world.
As for the AGP clock problem, a PCI vid is probably the best bet. 440BX has a 1/4 multiplier for PCI so you can keep PCI at 33 MHz with a FSB of 133MHz. Why on earth they didn't throw in a 1/2 multiplier for AGP is beyond me... I do have a couple of GeForce cards that are almost perfectly functional on the 89 MHz AGP speed, but they aren't perfect. My GFFX 5950 Ultra actually is pretty reliable at this speed. It's also the fastest AGP card you can put in this board with its AGP 2x 3.3v slot, aside from Radeon 9800 XT perhaps but I really doubt from my experience with Radeon 9700 that it would work at all at 89MHz.