Vesalia sells NOS A4000T disk drive modules, in case yours is busted. Other than that, try using a different floppy cable and see if there are any differences.
I've had a similar problem in my A4000D converted to Mirage 4000 tower, and after trying different cables, the drive worked fine. It turned out that all cables were working fine, but some didn't make proper contact with floppy drive pins. I finally found a cable that "touched" every single pin fine on the floppy drive and viola, it worked! It's really weird. Even after using a spare A1200 drive in A4000 for test the same problems were occuring, so that narrowed down the problem to either the cable, or the motherboard. Luckily it was the cable! :-)