First, this machine has no LBA controller so modern hard drives won't work with it. By modern I mean > 512MB. You need a hard drive capable of running in a mode that addresses the drive by cylinders, heads, and sectors. Ones not like that require the addition of an add-on card for LBA support, and at that the highest-capacity addon card for old ISA boards I can/could find was only 2GB.
Second, check the pins in the IDE socket. They bend really easily on this machine for whatever reason. If one is bent, cut the power and try to un-bend it with a flathead screwdriver.
Third, if you have one of the older-type IDE cables, you need to have the correct orientation of the cable and the motherboard (the controller on this machine does have the grooved top, but some old IDE cables don't). You might also try swapping out the cable altogether.
Fourth, make sure that the settings S2 and S3 are both set to OFF on switch SW502, located conveniently under the four ISA slots in this machine (have you figured out if the fourth one actually does anything with the backwards position it's in?)
Fifth, if you do have an add-on card for LBA functionality, make sure you have the jumpers where they should be, otherwise the HD won't be recognized.
Windows 3.1 should work fine, it is with operating systems requiring MMX extensions like 2000 that you'd have non-booting trouble. NTLDR and the DOS bootloader both are pure x86 assembly I believe so they should be able to easily boot as far back as a 386. The kernels are a different story, most modern kernels have MMX support (that 486s did not have). I recall running 3.1 on this machine for eons anyway. I assume the farthest you can go OS-wise would be 98 or NT, depending on which you find to be more advanced (98 has the full driver framework but NT has the full Win32 API... go figure, they split hardware and software support until Win2k).
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