Manual tranny - have you checked the clutch interlock to make sure it is working? Only other thing I can think of other than the alternator would be to check the battery cables to make sure there is no corrosion built up on them or even underneath the cable right by the cable end. Also, would be worth the time to check and make sure the ground cable is actually well-grounded and the other wires that are on the starter are firmly attached.

Other than that, checker and autozone (and Pepboys) all have equipment that they can use to test your alternator and your starter, too (IIRC). You might have to remove it and take it in though.

If you are having problems, and need some help, give a shout here or on the Trailseeker board and see if someone can help.