You found your answer to the resampling, so I'll just go to the next bit.
I just upgraded my e6400 Ultra from 4.02 to 4.70 last night. Made a back up of 4.02 first, then I followed the instructions in the OP
here to make the FlashPrep and EOS 4.70 disks. I got the FlashPrep from the E-MU website, but I could not get the EOS470.exe from there to copy to the floppy. I found a copy of the file
here and it copied over, and everything installed very quickly. I also copied both programs to floppies using Windows 7. Main reason I did the upgrade was so I could drop an audio file on Zip disk and then load it up on the E-MU. Tested a few files out last night, works great.
Only thing now is that my SCSI Zip drive shows up as several SCSI devices. It works, and my other SCSI devices work, but I need to figure out why it's showing up multiple times.