Hi Hubz,
I can probably contribute to this a bit since I have also been collecting some PC-98 games over the last few years, especially ones that I would love to see English translations of. Great job with this initiative by the way.
For now I can contribute the manual and glossary of Brandish 2. I can always provide scans later if you like.
http://retro-type.com/brandish/br2/The other PC-98 games that I have currently that are complete are:
Oerstedia
Magic ++
Slayers
Dragon Half
Xak: The Art of Visual Stage
Xak II: Rising of the Red Moon
Xak: Precious Package: The Tower of Gazzel
Xak III: The Eternal Recurrence
Fray In Magical Adventure
Tower of Cabin
Brandish
Brandish Renewal
Brandish 2
Brandish 3
Brandish 3 Renewal
Brandish VT
Popful Mail
If you are looking for PC-88 stuff as well, I have these so far:
Zeliard
Ys I
Ys II
Ys III
Popful Mail
XZR
XZR II
These will certainly take some time to scan all of these, but if there are specific ones that you might want to get first I can certainly try to start with those. Also, if you have the ability to clean up scans and align images correctly, this will make this a lot quicker for myself and others who may want to contribute to your project.
-Thomas