Good news, I've managed to prepare a ModTool scene than can be used to do FK animating for jk2. It's still very experimental and may actually not work too well with all models (in particular if a model is weighted to the face bone, since I had to add that one to the skeleton provided with the jk2 SDK, and it ended up not quite where it should be).
The scene is called CRUFTFORGIL.exp (it's pretty close to the actual BOTH_1CRUFTFORGIL stance, but not completly accurate at the feet, yet) and can be downloaded from
here.
Animation can done by selecting bones, rotating them (rotation tool is invoked through pressing 'c'), keying each rotation (pressing 'k' immediately after rotation is done - while the rotation tool is still active) and then advancing to the next key frame.
At the end, save the scene under a different name, then invoke File / Export / dotXSI, accept the preset export settings and save the xsi file somewhere.
To convert the exported xsi to gla, you'll have to use the carcass.exe which is included in the jk3 SDK (the one from the jk2 SDK just won't accept xsi's created by ModTool, even v3.0 xsi's).
I've prepared a little batch file that makes compiling single xsi's to gla a bit easier than using Assimilate (can be downloaded at the same place as the scene).
Uhm, there's one more thing you have to know: the weighting of the polygon mesh is slightly different from that of the actual Kyle model, so don't rely too much on how the deformations look in ModTool. Modview can be used to check them right after exporting / compiling.