Just getting back to this now.. there are a few things to look at when looking at online student systems. This one is particularily cheap but don't think it would accept online payments:
http://www.quickschools.com/
However these kinds of information management systems are out there. Luckily the processes that students go through from registration -> completion are in large part the same, so there are options for you now!
edit: ack, that one is per student per month. Lame.
