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400k Internal floppy drive out of alighment and only reads its own disks?

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So I got my parts for restoring my upgraded 128k. The 400k drive was completely seized up which is to be expected. But there is a problem. After lubricating the drive, it was making a continuous clicking noise. I found out that it was the limit switch that homes with head. It was to far away for the little notch to block the light. I loosend the screw holding the switch in place and moved it back a little. The drive homed properly. The drive reads and writes perfectly, But only its own disks. It will not read any disks from any other known working drive. I have multiple 400k formatted disks from my 800k drive. Not of them read, They just eject. I think that optical switch position was important as I don't think the head homes to the correct position to read the tracks. I got it to almost read one of my disks by messing with the switches position for a few hours, It almost fully booted but something was thrown off before it could finish. I connected the 400k drive to my 512ke with the scsi hard drive attached and formatted and transferred some software to its own disk. This disk reads perfectly and boots every time. 

The head looks brand new and I cleaned it with a q-tip and alcohol. IDK how to repair this. Its probably something really stupidly simple.  How do I fix this?  


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Not sure on the 400K but I know on the newer drives, you loosen the stepper motor on the rear of the drive, and physically rotate it until the alignment comes in. its VERY touchy and the adjustments are minute. Its easier to use a scope and watch the waveform come off of the disk and adjust for peak amplitude. 

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