As you may have already found out from doing research, transmitting sample or waveform data over MIDI is extremely slow, and not really feasible for larger files. You may want to look on Ebay for floppy disk drives that might be compatible. You could also look for a SCSI kit for your EPS and get a SCSI Zip drive if you can find any working units on Ebay. Good luck!
Just out of technical interest, do you have some reason to worry about the floppy disk drive?
I understand that the physical drives were made by Sony or Matsushita and would normally be pretty robust. The disks are DSDD, and they should be pretty robust as well. They could well last for a LOT of years yet. If you've been having problems, have you been using the HD type disks as DD? This is 'possible', but this alone is quite unreliable, you may just need to track down some of the older DD type disks.