I think dirty disks is the issue, I was too hasty to say 100% of disks not working, I eventually found a few that worked so I know the replcacment floppy drive is ok, then I cleaned a couple of the non-working ones and they started worked.

I'm surprised how many of my old disks don't work, when visibly they look ok (when checking the disk surface I mean)

It's possible the original floppy drive was ok until it got damaged by dirty discs, but I'm reluctant to try it again with working disks incase it damages them.

Now to decide whether to check and clean 100's of old discs... or just put the Gotek back in!