Does the drive still spin down if you power it on without the SCSI cable connected? if it does, then there's a problem with the drive. The old drives all should remain spinning as far as I know.
Even with the cable attached it shouldn't be spinning down. I have a bad drive myself, but it remains powered up and spinning even though the Mac gave up trying to boot from it. It doesn't tell drives to spin down last I checked. At least the Macintosh SE line doesn't. (I don't think any of the compact line does. Controllers telling the drive to spin down is more of a power saving feature and none of the old macs had much in the way of power saving features)
As for the 2.5 drive, it may not be terminated properly being that it sounds like you are using a 80/68 to 50 pin adapter on it. Also try using Lido. It seems my dead drive and gave me a useful error code that narrowed the problem to the drive and not the cable/scsi controller. If the 2.5 drive isn't terminated properly, Lido will give you a SCSI arbitration failed error. I forget the exact message, but I believe Lido will give you a clear error that can indicate a termination issue. If the SCSI bus is bad Lido might also display an error for that.
Although I may still attempt to format mine once my mouse arrives (as I can't navigate the program without a mouse.

). My drive had a head crash due to it's age. (it was inactive for a long time judging from the fact the previous owner said it was still working last time he used it but had it in storage for more then a decade)
Despite that, the drive does not power down even when connected to the Macintosh SE that boots to the flashing floppy disk icon. So your drive should not be powering down. There appears to be a serious hardware fault like a stuck head. Although some models that had a head crash might power down after failing to read the special area before track 0. Mine doesn't power down with that problem though.
Either way, if Lido fails to see/format your drive, a patched version of one of Apples official tools won't help.