No particular issue, I just wanted to recap what I figured out. It might help somebody.
I came across an old 5000D, decided to figure out what I could do with it. Decided I wanted to update it. Spent hours googling for "zaurus", "5000D", "rom" etc. Found the old Sharp Zaurus Devweb, it has some info and downloads for 5500. Found some notes that said do not flash a 5000D with 5500 roms, etc. Eventually I found the right roms on the ZUG front page - under "Site Mirrors" and "community.zaurus.com". I also got an email from Sharp directing me to www.sdgsystems.com for support - but their website doesn't offer much.
So I tried to flash the Zaur up to 1.38 by putting it on my only available CF card - a 128MB SanDisk. The green and yellow lights flashed on for 2 seconds, then turned off. Pressing full reset again brought the Zaur back. I read that early Zaurs had problems with the 128 SanDisks, so I figure it just didn't find the files to flash with, and aborted. The file was visible in File Manager though.
The file to flash (up to 1.38) is called "romimage".
The original version of rom was so early, that it didn't report what version it was in the settings menu (where everyone says to look). It showed the linux kernel version, though.
When I flashed it, I left the 256MB SD card in it by mistake. Didn't cause a problem though.
Now I'm trying to get the Belkin F506060 wireless CF card to work (bad fit for the Zaurus, it blocks the hole for the stylus). But, thanks to having 1.38 in there, the IRDA port is working!
Pretty cool, so far.
I found a lot of info on ZUG, thanks for all your posts!