Can the e6400 recognize that there is a CD Rom drive on the SCSI bus? One of the things that you need to do is set the software switch in EOS (ie the e6400) to allow computer on SCSI bus or something like that. It is in the manual how to do that.
It could be that the CD Rom drive in the G3 is not compatible with the e6400. If you don't get a drive showing up on the e6400 that corresponds to the CD Rom drive on the Mac, chances are that it is an IDE drive.
If you can't use the G3's CD Rom drive, you're best off to buy an external SCSI CD Rom drive. Don't buy the Glyph unless you really want it rack-mounted. I find them over-priced for what you are getting. I bought an internal SCSI CD Rom drive a few years ago and a case for it for $100 US. I'm not sure how much the Glyphs are going for but their regular external CD Rom drives are probably double that. In the end, you may save yourself some grief by simply buying a CD Rom drive for your sampler.
In regards to the hard drive, you can not use the hard drive of the mac. E-mu uses a proprietary hard drive format that is not compatible with any computer. It says this specifically in the manual as well. You have a variety of options though. You can buy something like a Zip (too slow IMHO), Jaz drive, external SCSI hard drive, internal IDE hard drive, or an internal SCSI hard drive. The Jaz drive is convenient because it is fast enough and, when you have it full, you can use another cartridge. With fixed disk hard drives, you need to backup to a CD when it is full.
The sound card is not important for the G3 unless you want to do audio recording in your G3. That is a whole other issue though.