Your low-lewel cd-rom driver in config.sys create 2 devices in ms-dos. MSCD000 and MSCD001 as example.
Now just use the /d and /l command-line switches for mscdex:
mscdex /d:mscd000 /l:d /d:mscd001 /l:e

Nope. It just creates 1 (mscd000 as example) (and it found 2 cdrom devices) and it assign the drive letter sequentially. I use generic cdrom driver oakcdrom.sys
So unluckily what you said doesn't work.

1) Try another driver, gcdrom.sys as example (plus this driver support SATA devices in DOS). If I remember correctly, this driver has /C switch.
So, in config .sys you have something like
device=gcdrom.sys /d:mscd000 /c1
device=gcdrom.sys /d:macd001 /c2
c1, c2 - IDE channels with cd-drives...
Then - mscdex with /d and /l switches...
2) Try /p switch with oakcdrom.sys.

use the master slave jumpers
dos assigns letters via :

primary ide master
secondary ide master
primary ide slave
secondary ide slave

http://support.microsoft.com/?kbid=51978

thanks for the help Gamecollector but still no luck.
And I have 2 cdrom drives on the same ide channel. I'll simply switch the master/slave jumpers on the 2 drives. Reading that microsoft document, the only solution. thanks Davros

I just don't have 2 CD-drives in my old PC - only 1. If I found another IDE CD-drive for testing - I tell you the results.