2) I will look into this for you when I get a chance. I've been very busy with a new job and moving house over the past couple of months.
3) This is very strange... I can't imagine why. There must be some specific check. I'll see what I can find.
4) Yeah. There's a check for this. It makes it so characters you can't have or haven't got through normal methods (GameShark or something) don't gain exp. Change the byte at 12E5C3 from D9 to E0 in a hex editor. This will bypass all of the checks.