Hi
Is the port busted. Put your Workbench disk in DF1 ... which I assume is your external floppy drive.. Then BOOT. Keep both mouse buttons depressed [ down ] and wait for the early boot screen. Select Boot Options. If DF1 is there then select to boot from here. If not or doesn`t work then probably the port is busted. I wouldn`t muck about.. Get a replacement motherboard from Ebay. Otherwise you will be struggling a touch.
Why not use IDEFix97 from the one floppy drive and boot from the hard drive... Unclear.
scuzz
http://www.commodore-amiga-retro.com