Cool! A Jeep with a frame, built during the Age of Steel! I think '91 was the last year for that machine. Does it have "Final Edition" badge on the dashboard? Some of those later models also came with an overhead console (from Chrylser's minivan parts bin?)
I think you're on the right path. You can pick up a reprinted factory service manual for about $50 on eBay. Go thru it from stem to stern and take care of all the standard maintenance items that the previous owners ignored. Most of it will be more labor than parts, and the parts are relatively inexpensive, like u-joints, seals, filters, and fluids. You'll end up with a reliably drivable vehicle -- then mod from there.
Yeah, the rear windows always seem to be a problem, due to the multiple electric switches involved. If you haven't already discovered it, here's a link to IFSJ's tailgate repair tips:
http://www.ifsja.org/tech/tailgate/
BTW: if you're shopping for shocks, Edelbrock is having a crazy-cheap clearance sale on IAS reservoir shocks:
http://store.edelbrock.com/universallifted.aspx
(Not everyone has good luck with these, so do a little web research.)
And Bilstien is having a buy-3-get-one-free sale on their shocks thru the end of April:
http://www.1freeshock.com/coupon.html
You're in for a fun, rewarding build! Wagoneers and Cherokees have a great history: Wagoneers placed first and second when they ran the old Sno*Drift rally, and have competed successfully in the Trans-Amazon rally (9000 miles!), and have been in all kinds of off-road and overland efforts.
Bill Harrah (of the Harrah's Casinos) had one built with a Ferrari V-12 engine. It was sometimes referred to as a "crime against nature" and was displayed in his Auto Museum:
http://www.trombinoscar.com/willys/jeep7701.html
The best part is the strong community of enthusiastic modders and problem solvers -- which now includes you! Have a blast!