Hey Jeff,
I'm also starting to use Dr. Spielbergs toolbox and I'm very curious to know the answer to your second question concerning the scanning sessions, because I have the same issue.

However, I think at least I might be able to help you with the third question:

From what I understand, it is not necessary to rename the functional files as long as the filenames and the file paths are consistent. For example: If you have the functional files for subject 001 stored in a folder located at C:/User/subject001/epis/4D.nii and the files for subject 002 accordingly stored in C:/User/subject002/epis/4D.nii, and so on, you will select the 4D functional file for the first participant and "the toolbox locates the rest of the files by replacing the participant ID".

I hope this helps?

HB