Yeah 3 short black screws for the gd-rom. If you use long ones and screw too hard you might break the motherboard (you'd be screwed ain't it ?).
Sounds like you've got it sorted, but for reference iFixit has good guides on taking apart the Dreamcast and many other consoles:- http://www.ifixit.com/Device/Sega_Dreamcast
Of the Dreamcasts I've taken apart in the last month not a one had longer screws on the GD-ROM. My September 1999 DC does but none of those done mid->late 2000 don't.
You really want to take more note of what goes where if you're going to disassemble something. If you're that bad at remembering, take a sheet of paper, make a rough sketch of the unit and poke the screws through where they go.