Hi Sinclair,
One thing I didn't specifically mention (although I intended to) was that the E5000 only comes with 1 CD Rom of sounds. They are about the same calibre of the 8 CD Roms that come with the e6400 IMHO. If having lots of sounds initially is important to you that may be one reason to go with an e6400 instead.
In regards to SCSI and your PC, well you will be able to transfer samples back and forth via SCSI. This is great if you like to do your sample editing on the PC. You cannot however, share your PC's SCSI hard drive for storing E-mu samples, Cubase songs, etc. The E-mu samplers use a proprietary format which the PC cannot recognize and vice versa. You really need a dedicated hard drive for the sampler or a Zip or a Jaz. If you go with a removable media drive, I would personally go for the Jaz since it holds more and is much faster for loading and saving than the Zip drive.
Chances are that your PC's CD Rom drive is IDE and not SCSI. If this is the case, you definitely cannot use it for loading sounds into your sampler. Basically add another $100 US or so in your budget for an external SCSI CD Rom drive. If it is SCSI, there is a chance that the EOS sampler can recognize it and load samples from it. I have not tried this so I don't know for sure. I guess you'll have to try it when you get it.
Good luck and enjoy. You won't regret buying this machine. It's great.
Fernando