Did you try plugging back the old VGA? Or no VGA at all?
Changes like that clear CMOS and resets the bios records for hardware. Can help sometimes.
Might happen that your windows will refuse to work if you change too much of the hardware. Part of anti-piracy protection. I call it anti-customer protection.
If your BIOS is corrupted, you can make w98 boot floppy with flashing program and BIOS that you need, and command lines can be set in autoexec.bat. The floppy controller part of the BIOS is one part that is more-or less universal, and if that part is not screwed up, you can flash the BIOS by booting it from the floppy. You won't see anything on monitor, or hear the HD, just floppy. That is, if it is corrupt BIOS that you have there.