No, never hack it up - there are only so many Amigas out there! Especially 3000s and 4000s. Keep them original.
I no longer have it in my 3000, but when I did Mech's SCSI card reader fit fine in my 3000's right-hand floppy bay and I could slide the PCMCIA adapter in and out.
I attached it to the drive sled using velcro since the screw holes would not line up given I wanted the drive pushed back as far as possible (so I wouldn't have to modify the 3000's case front).
Perhaps the velcro added enough height, I had no issue having the PCMCIA adapter protruding fron the front.
