I had this problem before, and I think it was software related, is there any way I can change the kernel of the hard drive that won't boot?

Only if the kernel was buggy, for instance, if you wrote it yourself. The factory kernel and Mark's kernels have not had any problems with the hard drives. It is highly unlikely that it's a software problem.

Most likely it's one of the hardware problems listed in the usual place. Did you read through that carefully?

From your description, my money is on the IDE header solder joints, or perhaps the drive itself being bad.