The first time I tried to fit the windshield onto the body last year, it was too narrow to fit correctly. At that point, I put it aside to deal with later.
Well, yesterday I decided that now was 'later'. After playing around with the windshield some, I realized a couple things: 1) Someone had welded a crack on the driver's side leg, so I had to grind that down a bit to help it fit; 2) The cowl of the fiberglass body was not shaped quite right, so I would have to 'trim' some of the rubber gasket to get the window to fit (the rubber needs replacing anyway, so I hacked it for test purposes — as can be seen in the closeup photo below); 3) Even with the rubber hacked, the windshield likely won't fit as tight as I'd like, but I can live without a tight seal as I doubt I'd be driving in much rain anyway.
With those decisions/concessions made, I had to choose where to drill the holes for the windshield mounts. The key for me was to get the right tilt to the windshield angle, making sure the horizontal part of the legs looked pretty level and making sure that when the windshield was tipped forward that it would rest level (something that I couldn't do after mounting the windshield to my first jeep). Finally, I had to make sure the windshield was back on the cowl far enough so that the windshield frame binders could be mounted to work correctly (I'm calling them binders here, but what do you call the two devices that pull down and secure the windshield?).
Another task I tackled today was the brake pedal. I took a brake pedal assembly out of a junk yard '90 cherokee. Originally, I had the pedals all set up for a clutch and brake pedal. After getting that setup complete, I changed my mind to go with an automatic. With that decision, I chose to get a wider automatic brake pedal. Fortunately, the cherokee's also came with automatics (and hence automatic brake pedals) and they used the same brake/clutch assembly system, so all I had to get was a brake pedal and resize it. So, if I do decide to switch to a stick/clutch, changing out the brake pedals and adding the hydraulic clutch mechanism (which I already have) will be a snap.
This might be a pretty good deal. 
