As part of creating a CoOp gametype for OJP, I'm also doing the the JKO maps as well. However, to keep the powers at be happy about copyright issues, I'm going to require the JKO cd to install all the nessicary files.

However, to do this, I'm going to need a install program that can install specific files from the JKO asset files. Any ideas/suggestions on how I can do that?

You could try NullSofts NSIS together with a plugin called ZipDLL.
I'm using NSIS for the DF Mod demo, but i did not try to use the ZipDLL until now.

I'm checking if the user has installed JA correctly in order to provide a correct default installation path.

I can give you my installer script, of course.

Edit:
NSIS is available here: http://nsis.sourceforge.net/)
ZipDLL here: http://nsis.sourceforge.net/archive/download.php?file=ZipDLLv1.2.zip)

Thanks Fracman, I'll have to give it a try.

Fortunately, it looks like I won't have to totally disassemble the .pk3s to use them in JKA because things work correctly when you copy them whole hog.