Someone can correct me if I'm wrong, but...

The Mac OS ROM shouldn't be a problem. I have a G4 MDD that is running on a rom 10.1.1 (I think? 10 something, whatever's on the 800MHz eMac disc here) so my guess is that the rom isn't the problem. You might check to make sure that it's compatible with booting OS 9. There were three different revisions of that model, and the second one with the FW800 doesn't boot into OS 9. This seems the likelier reason you can't get it working.

edit: http://www.megaupload.com/?d=XIZRTZXW
(has the older version of that rom just in case it helps you somehow)

Here is a good start ...

http://macintoshgarden.org/apps/macintosh-system-922-1021-power-macintos...

From my MDD's CDs (http://macintoshgarden.org/apps/macintosh-system-922-1021-power-macintos...), might be safer to just use them to clean install 10.2 and 9.

And the link to the ROM from the MDD set (9.6.1) http://www.megaupload.com/?d=MT4DOQKV

Hope that helps. Make sure you have OS 9 on a sub 200GB partition.

Well, the Mac OS ROM v9.5.1 or v9.5.2 or v9.6.1 are definitely the right ROM file for your MDD. The v10.2.1 file may or may not work. It may already work for other Macs, doesn't guarantee it'll work on your MDD. I've only seen the Mac OS ROM v10.2.1 in OS9 System Folders for Classic, not for booting OS9.

If you burn yourself a set of install and restore discs (always handy) from the page linked to earlier, you don't have to install OSX 10.2 to then install OS9, you can just run the OS9 Install (it can only be done as a partial restore) from within OSX, any version of OS X greater than (and including) OSX 10.2, even OSX 10.5.

Well, can we assume that you have some version of OSX already installed ?
And if it's OSX 10.3 or 10.4 or 10.5, did you install OS9 Drivers when you formatted the disk ?

If so -
Download just the "Mac OS 9 MDD DMG" link.
Lock it.
Mount it.
Drag the contents of the mounted volume to the top level of the disk you want to use to boot OS9.

If, however, you don't have a version of OSX installed already, you'll need all 6 disc images - the two OSX install and the 4 restore: Then install OSX 10.2.1 and run the restore while booted from the OSX just installed. You can select to do just a partial restore of OS9, which sounds like what you want.

http://macintoshgarden.org/apps/macintosh-system-922-1021-power-macintos...

I'm trying one of the links above currently, although it requires an install of OSX first

The linked page (above) contains a series of download links.
There are 6 links for the original disc media that came with the MDD, made up by (2) OS X Install disc images and (4) Restore disc images.
Whether or not you currently have a version of OS X running on the MDD, it would be worth your while to download and burn these 6 disc images to CD.
Along with those 6 links, there is a "Mac OS 9 MDD DMG" link.

If you have any version of OSX already installed on the MDD,
Download this "Mac OS 9 MDD DMG".
Lock it.
Mount it.
Drag the contents of the mounted volume to the top level of the disk you want to use to boot OS9.

If, however, you don't have a version of OSX installed already, you'll need the 6 disc images and you'll have to perform an OSX install and an OS9 restore (while booted in OSX).

Again, did you install OS9 Drivers when you formatted the disk you're going to use to boot from OS9 ?

Forget all about the Mac OS ROM for now, the Mac OS ROM file that come included with this "Mac OS 9 MDD DMG" image is the correct one for your MDD.

If you're still trying to use the OS9 System Folder you already had on your external drive (just found your post in the Apple Discussions), it's because it's meant for running Classic, not for booting. Your original stipulation that you had Mac OS ROM v10.2.1 indicates that this is the case,

Yes, 10.4 or 10.5 will be fine.

Mac OS ROM file at v9.6.1 is maybe because that is what was included in the downloaded disc image. Mine is v9.5.1 - that came with OSX 10.2.0-era MDDs.

Reckon the disk was missing OS9 drivers.