Hello Vogoneers! What a rigmarole I've been through.
Firstly I'd like to thank everyone who helped me out picking system parts and deciding on the gfx card to use.
So this build has certainly been interesting, I went with the 3dfx Voodoo3 2000 16mb PCI which works great! (Now the system is working...)
Firstly I got the system running under pure MS-DOS 6.22 with Windows 3.11 and updated the bios to the latest available with large drive support (F7b). Along side this I had installed and configured a IDE SD card adapter with a 64gb SDXC card which had a separate fresh FAT32 partition with a untouched Win98SE on it. It all worked fine. Got networking working in Win3.11 (winstack) and in DOS (Realtek RTL8139 packet driver). Played some quake world in dos with a nice near 60fps at 320x200. I improved this using a DOS Glide version of quake along side MXK6OPT.exe - A K6-2 video memory access optimiser. All seemed good but then I ran into problems with the Sound Blaster 16 (CT2230 ISA) as described in a previous post the digital effects would cut out leaving only the MIDI playing in games like DOOM/DII and Duke3D, I couldn't fix this problem. Multiple re-installs, different Creative drivers and Bios setting changes didn't fix it.
While looking for a solution online I found one post on a random site describing a similar problem dated around the year 2000, their fix was changing out a Seagate HDD which apparently was interfering with the card?! It was the only thing left I could try, so I gave it a go. In the process of copying the Seagate HDD (ST340810A 40GB) and swapping it with another the drive lost two pins (pin 1 and pin 38) the solder holding the pins in place had crumbled away leaving the pins in my external drive adapter 😠.
So I moved onto a fresh drive and planned on doing a fresh install... Drive un-able to boot off, stuck at 'Searching for boot record on IDE-0... OK'. I tried about 6 other drives same problem. Boots fine off DOS floppy and can browse and install to C:\ on all of them, but BIOS cant get past 'IDE-0...OK' when booting directly off the drive. I though well I'd broken the mother board or something, re-flashed the bios same results. Plugged the SD card IDE adapter back it, it boots!
So now I'm running Windows 98 SE with dos 7.1 configured as per Phill's video here http://www.philscomputerlab.com/ms-dos-mode-tutorials.html everything runs perfectly, made a copy of the install because I know Windows 98 can be a pain with corrupted system files after crashes or even just installing drivers, Glad I did too. So getting 3D Windows games to work was the nightmare i was expecting, not because of Drivers but just Windows in general. DirextX, Windows 98 UnOfficial SP3, IE5/5.5/6 and 98Lite just lots of things that didn't want to play well together.
It's now all working! Heres what I did/have in TLDR form:
The Build:- Same as first post but with 128MB of ram and Voodoo3 2000 PCI 16MB.
The System & Install order:- Windows 98 SE, Drivers for LAN + Sound + Amigamerlin's 2.9 3Dfx Drivers (highly recommended!), updated IE 5.5 then 6, UO SP3 main update, DirectX 8.2, DirectX 9.0c. This is STABLE.
As for the sound issues in DOS, digital effects in Doom/DII still cut out after a while, but it's much much longer (about an hour now as opposed to 5 mins). This doesn't happen in Windows only in DOS MODE, so must be caused by the dos drivers alone. Since both Duke3D and Doom work in Windows I have no problem with this.
EDIT: This problem persists even into windows, but only when running DOOM/DUKE3D after an hour or so, It also kills all wave effects in Windows. A reboot fixes it. Not sure if Driver issue or fault on the Sound Card, I'm leaning towards Driver or Bug as disabling the hardware in Device Man and enabling it again fixes the sound.
The only game other than them causing me trouble which is still a mystery is Rogue Squadron 3D, in one earlier unstable install of 98 it ran fine when patched to the latest version in Glide mode (not so much D3D which errored on launch). Now on my stable system it will only run un-patched at v1. Patching it causes the menu not to work which is apparently a problem with DirectDraw, but the game now does run in both D3D and Glide mode. I'm fine with not patching the game so this is a moot point.
Benchmarks coming soon. Will also test impact of additional RAM over the cacheable limit. Cheers W.