Things to try:
Try setting reserved drive letters in device manager
Change partition on USB to logical (haven't tried it but might work)
Try Letter Assigner Re: Need help with Windows 98se and drive letters
Add another drive HD/SD/etc (internal or drive caddy) with enough space to system
Possibly monitor registry access while assigning drive letters and see if you see something

The best option is to simply use an actual SSD. USB drives quit working in Windows - not due to drive faults - after being connected/reconnected a number of times, due to the registry being stuffed with new entries. I had to go in and delete registry entries for USB drives many times, in order to get Windows to detect them properly again, because there were simply too many entries - for the same device - in the registry. You can easily use an IDE-SATA adapter and SSD or get a PATA SSD, to use for your games.

Thank you for the help.

I cannot add another SSD sadly enough since that would mean having to give up my physical CD drive. The interface I used to convert from SATA to PATA only works with a single device on the ribbon cable. Even adding an SSD and a CD drive makes neither work. I went for USB because, unlike SSDs, it needs no TRIM command in Windows AND you can go as high as you want to for size. I went with 128GB for price but you can get a single 512GB to work too. Without modding Windows 98 you can't do that with SSDs. The max is 120GB before you start overwriting data.

I'll try the other tips though - but the USB stick thing needs to remain. It also makes it way easier for me to swap files back & forward between my main PC and my retro PC and with USB 2.0 it's as fast as I need it to be.

DosFreak wrote on 2021-10-27, 16:33:

Things to try: Try setting reserved drive letters in device manager Change partition on USB to logical (haven't tried it but mi […]
Show full quote

Things to try:
Try setting reserved drive letters in device manager
Change partition on USB to logical (haven't tried it but might work)
Try Letter Assigner Re: Need help with Windows 98se and drive letters
Add another drive HD/SD/etc (internal or drive caddy) with enough space to system
Possibly monitor registry access while assigning drive letters and see if you see something

Well, it seems while reserving the drive letter for the emulated drive didn't work, reserving it for the USB sticks DID. So my problem is fixed, thank you!

red_avatar wrote on 2021-10-27, 17:12:

I went for USB because, unlike SSDs, it needs no TRIM command in Windows AND you can go as high as you want to for size.

if you're only storing ISOs on the SSD I wouldn't worry about that anyways, not like you'll be constantly writing data to it.
you can always stick it into a modern PC for writing to it anyways.

imi wrote on 2021-10-27, 19:37:

red_avatar wrote on 2021-10-27, 17:12:

I went for USB because, unlike SSDs, it needs no TRIM command in Windows AND you can go as high as you want to for size.

if you're only storing ISOs on the SSD I wouldn't worry about that anyways, not like you'll be constantly writing data to it.
you can always stick it into a modern PC for writing to it anyways.

Well moving CD i mages quickly forces you to TRIM. My 120GB SSD was as good as full before I moved the images to USB sticks.

But the current solution is best: PCI card with 4 USB 2.0 ports, powered by a 5V cable. Then 3 USB sticks in those ports, each holding a range of CD images. In total I estimate I'll need some 300-400GB for all my Windows 9X games (many are multiple CDs and Alcohol uses about 10-15% more space than the CDs themselves) so 3 sticks should be about enough. Each stick has a fixed drive letter now and is easily removed or replaced.

I mount over the network and install and crack, haven't tested cd audio yet over the network though if an issue I'll just copy locally. Constantly in fear of freenas dropping pre smb2 but it's still working. (When it is dropped will just have to copy locally via sftp 🙁 )

This is why I avoid to install games from a CD drive with letter D.
I quickly change CD drive letter to Z after installing Windows 9x to avoid this problem (in device manager, properties of CDROM drive).

This also can be done with virtual CD devices.

Disruptor wrote on 2021-10-27, 20:34:

This is why I avoid to install games from a CD drive with letter D.
I quickly change CD drive letter to Z after installing Windows 9x to avoid this problem (in device manager, properties of CDROM drive).

Well, some games are weird and refuse to play CD audio because for some reason, they look at the D drive only for CD audio, even if I changed default drive to E. Still, it works so I'm happy.