> (1) Do the input files need to include the participant's IDs?
Yes, any characters including numbers such as those in your 3dMVM script would be fine as long as they can differentiate the subjects.
> (2) I am not too sure what the main difference between using the glf and glt is
GLT is pretty much all you need. GLF is mainly for cases when you want to examine the differences across three or more levels of a factor.
> (3) Does the general set up of the code looks correct (pasted below)?
You need a backslash (\) for the following line in your 3dMVM script:
-SS_type 2 \
Type 3 is more popular.
Gang