Windows 98 Hang at startup

I am working on fixing up an older computer that has
Windows 98 first edition. I had to replace the cdrom and
the floppy diskette due to them both failing at one point
or another. I had my main harddrive from my other
computer running as a slave so that I could transfer some
files back and forth quickly between the two drives. When
I removed my hard drive and reset the jumpers on the back
of the main drive, Windows hangs after it loads all the
programs in startup. It will hang between 5 to 10
minutes, and then it hangs intermittently after that until
it comes up with an explorer error and closes out. When I
reconnected my hard drive as a slave, the computer booted
up fine; no slowdown, no hangups. I have checked the
win.ini in the msconfig, and also made sure all the
startup programs worked properly. I am severely stumped.
please help if you can.