Update:
System is currently running agreeably other than two issues that I'll go into after explaining the recent changes and posting what I expect to be the final spec.
AOpen AX6BC
PIII 550MHz
512MB RAM
Creative CT5823 TNT2 32MB AGP
[RME Hammerfall Digi 9636/52 PCI]
AOpen AW744L II PCI
SB LIVE! PRO VALUE CT4830 PCI
Promise Tech Ultra ATA/66
10/100 Ethernet PCI
* ISA BLOCKED BY PCI *
Adaptec ATA-1505
Toshiba 6x DVD-ROM
LG CED-8083B 32x4x4 CDRW
*3.5" 1.44MB in 5.25 holder
*TEAC FD-55GFR 5.25"
ZIP250
Fujitsu-Dynamo 1.3GB MO
20 GB PATA
80 GB ATA100
I had to replace the startech ATA/100 because one of the two ATA ports was bad, and after trying another one from another brand I saw the promise tech brand on ebay, and the sticker on the rom triggered a memory, so now I have the same card in my system that I had as a kid. Works fine with the 80gb ATA/100 drive. Second plug on the card is dedicated to the removable MO and Zip drives because I needed to connect the 20gb PATA drive directly to the motherboard to boot right with the previous cards and figured it was easier just to not bother swapping them because there's no benefit to using a non-ultra ATA drive on the card anyway.
Which leads to the next issue that I've discovered. After trying new cables and either drive, I swapped in a different ALPS 3.5" drive to test that as the sole floppy and as far as I can tell there is something wrong with the floppy port on the motherboard. Which means that I'm still without any way to make floppy disks on the system for my old synths and samplers, but at this point I figure the W30 can be imaged to be used on a GoTek and the VFX is going to be what it is with the GoTek. The MSX might even be easier. The * means installed but not connected.
I still have problems with the ATA-1505 needing IRQs that have to be occupied by other devices, I'm not sure if there are any ISA PNP SCSI cards with 25-pin ports on the back out there but if anyone knows of one, let me know. It's not necessary so it's disabled in win98, with the correct drivers installed but an IRQ problem.
For some reason the ethernet will not pull an IP from DHCP. It worked fine in previous installations, the drivers are the same and the lights show that it's connected and it pulls a 169 address (no response from DHCP, but cable is connected). I assume it's a problem with my router that I'll have to look into.
The Digi 9636/52 PCI are expensive and not immediately necessary, so the slot remains empty ([brackets] mean waiting) and I've got the win98 drivers available. I know that I need that card specifically not just because of the period-correct aspect but because I have 2 'blackface' ADATs for recording and it's the only card I could find that has 2 sets of lightpipe interfaces and the descendant is still the top rated internal audio interface by Sound on Sound magazine.
Current system runs very well, the 20gb drive provides an IDE boot hard drive along with the two optical drives direct from the motherboards and the 80gb drive runs off the Ultra ATA interface. The Ultra ATA interface should be bootable but I haven't bothered since everything is functioning as is and I've rebuilt/remade the system as much as it is. Halflife, Unreal Tournament, Re-Volt, and some other graphics-intensive games work great. Sound from the soundcards is completely functional and easy to route in software. DOS games seem to work ok but I need to have space to fully set up the system to test audio compatibility and frankly that's not the point of the system anyway.
Future ideas are to look into swapping the SCSI card for something to provide an FDD interface, because I have a parallel version of the Syquest EZ-135/EZ-230 drive that I've got for my W30 that I know works on Win98 machines. I'm not sure that the IRQs could handle an IDE floppy/ide/serial/parallel card though.