Incorrect Disk II connection - How bad?

Sounds like you may have blown the read/write chip and maybe a diode on the disk drive II analog board. The chips are socketed, but the small diodes are soldered in. Being a diode they have be put in the same way. Make sure the black band is at the same end as the other you take out.

Best to pull the cover and look at the analog board with a large magnifing glass. Too see if any thing looks bad.

You should be able to see any damage to the diode, the yellow center will look black. The chip maybe. Sometimes you can, like a top blown off. I do not off the top of my head what the number of the chip is. But they are not real cheap either unless the price came down they are about $8.00.

Hope this helps

Edit: this is the text cut from an archive of the FAQ -

I accidentally offset a row of pins on the //e disk controller card when plugging one of the drives in. Snap, crackle... you get the picture. I opened up my freshly fried Disk II, and in the center of the board there is a 74LS125 that is blown. Replaced it (it was socketed) with the same chip from another Disk II, and voila! it works again.

I would assume that misaligning the drive connector on the controller is what blew the 74LS125 in several Apple II drives before they got to me. Note
that while the genuine Apple Disk II simply lights the LED and doesn't move the
head at all when this IC was blown, a Mitac drive actually ate disks. So any
number of dead Apple II drives with different symptoms could have a blown
74LS125.

This is an archive of the FAQ entry:
http://web.archive.org/web/20060718212136/http://home.swbell.net/rubywand/Csa2FDRIVE.html#012

Great, you should have a ready supply of 125s on hand at all times.

I mentioned in my first post, which I had to edit and had enormous trouble with the AppleFritter editing interface... anyway, once your drive gets into this state, it will eat floppies. Everything you insert will be instantly erased, even if it has a write-protect tab. Always be very careful aligning the pins on the header. Be paranoid about it. Use a bright light, and triple-check the alignment.

I got a disk II from eBay that had a popped C4 with the same symptoms. It turned out to be the read amplifier chip (probably in addition to the cap and the '125). I ended up getting one from Newark as a special order and of course found some on eBay for less once I had placed the order. I made a blog post about it as well: http://phantompinecone.wordpress.com/2011/02/01/resurrecting-an-apple-disk-ii/

I hope that's helpful.