Wanted to report back this morning... I have the GUS PnP working in Windows 98 now! I can't say exactly what I did that caused the fix as I have been messing around with a lot of things.
1. I completely removed all entries in the Autoexec.bat file that Windows98 uses.. I think when I get to DOS though ill start by using the ULTRASND folder from the Orpheus website, more to come there. But for now, it looks like everything works without anything in the Autoexec.bat. No orphinit, no ultrasnd.bat.. nothing. Although I will say I may put orphinit back in to set audio levels, they seem rather low to start.
2. I re-installed the Crystal drivers.. not sure this really did anything but wanted to just make sure there was no issues there.
3. I ran Prepgame in the Duke3D directory. Maybe this fixed Duke3D the most.. not 100% sure as I changed the autoexec.bat in #1 and did this at the same time before testing the game. I didn't have to run that for Heretic though.
4. All IRQ's and DMA's are set to 7 in the Ultrasound properties and config. Soundblaster still shows DMA 1 but that should be disabled and shouldn't matter.. doesn't seem to have any effect anyways.
So with all that said, everything appears to be working great in Windows 98 and Windows 98 DOS Mode. I have tried Duke3D, Heretic, Epic Pinball, even Tyrian (need to run the ultramid.exe -c before launching as stated in the previous post). But they all worked well!
I also confirmed all the SB components worked as well still. The Digital Effects and OPL3 all worked normally still. I could easily switch and mix and match components in the Duke3D setup sound config (this is the best place to test things imo, lots of options and can test sound right away).
As of right now I don't think there is anything else I need to do in Windows 98 itself, everything is working properly. Next will be getting the actual DOS config setup and working properly, will report back on how that goes soon!