Perhaps you should stop messing with the registry and other start up things if you don't know what half the files are or do.
I mean safe mode is pretty self explanatory. It disables everything apart from the bare minimum to get the system to boot in to windows.
As for Win 98. I think it's time for a new PC
my current PC will boot in to Win 11 from power on in about 20 seconds ready to use. Though that mainly down to how fast modern NVME SSDs are.
640x480 would literally hurt my eyes. My smart watch has a better resolution than that.
As for the window and text, can't you widen or narrow the menu box by clicking and dragging? I know thats a thing now buts 26 years ago I can't remember.