I managed to put together a solution for the CD burner. It's not as clean as I would have liked, but I can now archive my source code reliably for the long term.
I picked up a Yamaha CDR-100 burner (prom rev. 1.12) and a SCSI-1 external case on ebay. I downloaded both the source and the pre-compiled copies of "mkisofs", "isosize" and "cdwrite". I was able to recompile the "mkisofs" for my machine, but I got errors when I tried to do the same for "cdwrite". NOTE: "cdwrite" is pre-compiled for the burner to be 'sc1d3' - I was able to open the compiled version using "jot", select long menus and 'search and replace' 'sc1d3' with 'sc0d2' (my drive was set for SCSI controller 0, device 2).
Some of the files I was backing up have names longer than 32 characters so even setting the RockRidge format option didn't take care of the filename truncation issue. What I finally had to do to maintain my filename structure was to "tar" the source directory to a file. This was then moved to an empty directory.
Next I ran "mkisofs" on the directory and created the ISO9660 formatted file. Finally I had to change to ROOT and "cdwrite" the ISO9660 formatted file. What ended up on the CD was just the .tar file. Multiple .tar files could be installed in the directory before "mkisofs"ing the directory - just remember the size limit of the CD is 700 Meg.
I hope this helps anyone else stuck using these "old" machines. My whole reason for doing this was the unreliability of the 4 mm tape for long term storage - I had 8 copies of source code for flight simulator visual databases made in Jan. of '98, 4 of which turned out to be unrecoverable. As flight simulators tend to have a lifespan of about 25 years I needed a more reliable long term storage solution.