I don't see anything that jumps out at me, but i will make a few suggestions:
BASEDEV=BOOTDLY.SYS
should follow the SCSI driver:
BASEDEV=AIC7870.ADD
Note that the default delay is 20 seconds. That can probably be, safely, reduced to about 5 seconds by adding /D:5 as a parameter. The delay is there to give the driver time to initialize, on fast machines.
For FAT32:
IFS=C:\ECS\BOOT\FAT32.IFS /CACHE:2048 /H /Q /EAS
CALL=C:\ECS\BIN\CACHEF32.EXE /S /F
I suggest removing the /EAS parameter. That also removes support for extended attributes, but they are rarely needed, and it will reduce the number of compatibility problems that you will encounter. I also suggest REMing the CACHEF32.EXE line. FAT32 works MUCH better (and even faster) when you don't use the cache.
Make sure that all of your *PATH* lines are ended with a semi-colon (

. This is just a "nice thing to do", but it is consistent with what eCS seems to insist on.
If you don't have a USB floppy drive, change:
BASEDEV=USBMSD.ADD /REMOVABLES:8 /FLOPPIES:1
to:
BASEDEV=USBMSD.ADD /REMOVABLES:8 /FLOPPIES:0
Since you are planning to use a virtual machine, it may help to change:
IOPL=YES
to:
IOPL=NO
That will give the background processes (your real system) better access to the disk when you are running the virtual machine.
I suggest REMing the line:
RUN=C:\OS2\SMSTART.EXE
That program is only useful to administrators of large networks (if they are dumb enough to try to use it). It simply causes problems for the rest of us.
I think you have looked at this, but read the Danis506 docs for a better way to handle the RSJ setup.
Last, you may want to try my LCSS (Logical Config.Sys Sort) program. It is at HOBBES. What it does, is sort your CONFIG.SYS so that it is easier for a human to read it. The machine has no trouble sorting it out for itself in either format. Be sure to read the instructions, especially about comment lines.
As I said, I don't think there is anything there that will affect your CD drive, but none of it should hurt.