Oh no....

I'm sorry to say this, but I think you may have just fried your Classic II's SWIM chip. The Apple 5.25" Drive should NEVER be connected to any Macintosh for this reason, save an LC with an Apple IIe card.

Have you tried using a floppy in your Mac's internal drive since? Its an easy enough mistake to make, especially with the same connector and all, but as I said, I think your Mac's floppy controller is gone.