Current rabbit hole (keep in mind this is my 2nd unit dedicated to win98se, so its microsd connector is broken off and I have to clamp down the card so that it keeps contact. I'm using a SOIC-8 programming clamp for this, perfect size and pressure!)
-Backed up the old 2GB+27GB microSD card with the 'ugly win98se' state of affairs with win32diskimager
-Wiped the card, reinstalled a known working DOS card contents 2GB+2GB+2GB+1.4GB with win32diskimager
-Erased D: and dumped the win98se Cd contents (mounted with SHSUCD in DOS) to D:
-Installed win98se with less issues, but it does at some point complain about a PCI device with 32-bit compatibility that it can't have and halts, here's a screenshot

Is it how I initally formatted the card to get to install win98se? I had my primary C partition as FAT16 in order to install dos. In my old card, I let the windows installer deal with the rest (27 GB) and I assume it formatted it as FAT32. With this image from my DOS setup, everything is in FAT16.
So, maybe **another** reinstall if I can get 2 microSds plugged in at once, one through the regular means and the other with a USB-card interface I have? I try that, the bios seems to like it (I wiped another 4 partition cloned card, built 1 new partition over everything, but it still detects 4 partition? Maybe as issue with the software I used), but windows BSOD complains about it before completling its bootup.
Current status: chicken and egg paradox to get a proper, fat32 win98se installation done natively on this machine, not through a VM or something else.
edit - I properly recreated the one partition on the 2nd card plugged by USB, it still detects a new hardware for this usb drive, still get a Fatal Exception 0E in VXD NTMAP(02) + 00000ABA.
edit2 - booted in command line safe mode, trying to format over this 2nd card which is detected fine there. Scandisk complained it had a bad LBA something something.
edit3 - uh oh, format goes to 100% but then gets stuck at verifying 0%
Edit4-I met a new friend. His name is setup /is to skip scandisk during win98 installation. I've got the single partition 32Gb in the main drive socket and I was able to use the BBS boot up menu from the bios (spamming F11) to boot from the other 4-partition card and get the setup going for yet another install
Edit5- Damnit, booting with the 2gbx4 (occupying c, e, f and g) and letting d run its own setup from d\win98ins lets me do the first part of the installation process (file copying) but it will just refuse to do part 2 after the first reboot. It loads to a black screen and flashing underscore character. This partition can't self boot at this juncture yet...