My diagnosis was wrong, it was not the SD-to-CF adapters (though those are still a problem with this system.) Something about this system, I am now assuming the motherboard, doesn't like it when I install Windows with two CF cards installed. I even swapped out the dual CF-to-IDE drive for a Startech single CF-to-IDE drive and slaved the PCI slit CF-to-IDE card that came with the system I harvested the parts from. So every single time I have tried to install Windows with two CF cards and the two Magicspin DVD DL burners installed and all connected to the IDE ports on the motherboard, the IOS error occurs after the first reboot. Windows successfully installs and I get to the first normal boot which installs the monitor driver and displays the Windows 98 welcome box with the funky music. After shutting down/powering back on or rebooting from this point, manifests this IOS error and I usually end up having to reinstall Windows again after trying everything I can think of to diagnose the error and fix it.
I recently successfully installed Windows 98 by having only one CF card and one burner installed, and then installed VIA 4in1 4.35 (the later revisions did not help,) DX7 and the Voodoo5 driver, backed up the Windows CF with Macrium, and then added the second CF card and burner and the Audigy 2 ZS. I was playing games and everything with multiple reboots at this point. However, I was having difficulties with the VXD driver and was tryinhg to fix that which started causing Windows to reboot whenever trying to switch between VXD and WDM drivers. I removed all but the Audigy 2 ZS and the Voodoo5 when coming across this thread and reading it and saw I may have screwed up by having my AWE32 installed when I tried to deal with the Audigy:
Guide: Installing Windows 9x and DOS drivers on Audigy cards (version 3.1)
I downloaded the ISO, but it was giving me errors when trying to install the first part as per the instructions, and then the reboots, so I figured something broke and that I need to reinstall Windows again. However, I forgot to remove the secondary IDE devices and the IOS error came back, which sucks but I am glad to get closer to figuring out what is going on and know that it wasn't the SD-to-CF adapters. No one has replied to any of these, so I assume that I am dealing with an extremely unique and isolated issue. I know others on here have the same motherboard revision and have not had these problems. I will say that my DVD burners act strangely when Windows is working and take forever to let me access discs when they are first put in, with the drives going VRIM-VROOM-VRIM-VROOM for a long damn time before I can access them, and turning off DMA reduced this problem, but did not eliminate it. Maybe these "Magicspin" drives are the culprits. Another thing is that only one of them appears in device manager. So, either the IDE ports/controller is messed up (but works under the right circumstances,) or these DVD drives have something weird going on...
I am still hoping for insight and/or answers, but for now I am reinstalling with ONE CF card and ONE drive... (A complete different DVD-ROM, at least for now.)