So I've found this solution to work a little better.
Here is what my .m3u files now look like for games that have the loading issue:
/home/pi/RetroPie/roms/x68000/.discs/J.B Harold Murder Club DX (Disk 1).dim
/home/pi/RetroPie/roms/x68000/.discs/J.B Harold Murder Club DX
/home/pi/RetroPie/roms/x68000/.discs/J.B Harold Murder Club DX (Disk 2).dim
/home/pi/RetroPie/roms/x68000/.discs/J.B Harold Murder Club DX (Disk 3).dim
Instead of re-numbering the discs like I mentioned above, I just put in a path for the second line without a disk number of a file extension, so at least when I go to use the Disk Control system, and it asks for "Disk 2" I can on "current disk index" and it will give me the names of all the disks, and the names should be correct for the disk it is looking for, I just ignore the one without a disk number.
That's the best work around I can come up with so far unless someone has any other ideas on how to get these multi-disc games to load that seem to hang in lr-PX68L when it tries to load a disk into FDD0 and FDD1.