Original/replacement parts for general repair are available anywhere as these engines where used by Jeep for many years. In terms of transmissions and transfer cases, you can find original parts but you also have several options to pick from as Jeep bits and pieces from the '90s and 2000's can be used with minimal or no fabrication/modification.
If you are going to press an Eagle into a daily driver role, then you have to expect the same level of maintenance and repair work that you would of any 30 year old vehicle.
Biggest stumbling block that I'm aware of are the IFC half shafts. However, even there I've read there is an option. Seeing how I don't own an Eagle myself (
) I'm sure several people with first hand experience will chime in and shed light on the subject.
There are a few options with upgrading the distributor/ignition and the carb. It all has been documented here on the forum...has anything else you would want to know.
Congrats on your pending graduation. If you want to dig in to working on an old and classic workhorse, the Eagle is a great choice. You'll learn a lot just from performing functional and satisfying upgrades. For example, when I do land an Eagle, I'll convert it to fuel injection and a stroker...if not a V-6 altogether. That might be more fab work then you are looking to get into, but a project like this can take you as far as you want to go. Let the good times roll.