Ok, my 2cents worth...
SuperMicro used to make a full-size AT motherboard, model P6DGH. Dual Slot1, up to 600 MHz I believe, 440GX chipset (holds 2GB of PC100, vs. the 440BX's 1GB max). Nine PCI slots, 2 ISA slots, 1 AGP slot, onboard dual-channel SCSI, RAIDport option.
Trouble is, it cost about $800 when I last checked. It's also *full AT*, which means it is an enormous board (about 12" by 13") and requires a suitably enormous AT case. The case SuperMicro recommended for it was the SuperMicro SC-801 AT chassis, which is also enormous and expensive (around $400). This chassis is actually manufactured by ChenMing, as are a lot of SuperMicro chassis.
I'd really advise you to go with ATX though. AT still has its place, mainly where many, many expansion slots are needed (I.E. backplane/SBC combo) or where motherboard space is very, very tight (certain lunchbox and compact rackmount chassis). For anything else, ATX is pretty much superior, and by sinking money into AT, you're sinking money into technology you may be hard pressed to use in the future. You're already feeling that now with this case of yours...
------------------------------------------------------------
"Eat a live frog in the morning, and nothing worse will happen to you for the rest of the day."