Ha - we're getting closer to the source of the problem!
If you replaced the battery, but didn't set the BIOS settings back to where they should be, then that might explain the lack of functioning MIDI.
The settings can be found here:
http://www.sonido-7.com/d8b/files/hdr_a ... b_bios.pdf
What did you compare it to, when you determined that the MIDI and Ethernet cards weren't in their right slot? If it still doesn't work with the new settings, then it might be worthwhile to put the cards back to where you found them... just in case that was where they were supposed to be after all.
Again, good luck with all of that!