Re: Advice on a build up.
First, to find out what size engine you have - there is a flat spot about 1" square just above the passenger side engine mount that will have the engine size and serial number stamped in it. One other way to tell is to remove a valve cover, and the engine size is cast into the head. On engine swaps, everyone has his own opinion, but if it were me I'd swap a 392 into it if the 304/345 isn't powerful enough (it'll have about 350 ft/lbs stock). On your body work, fiberglass sounds nice, but the price tag was always enough to scare me away (5K+ vs. 1200 for a good metal tub). On the transmission, keep your eyes open for someone parting out a Scout - that way you can pick up the clutch pedal and linkage and transmission cover at the same time. Can't help with the reverse shackle question - I've never bothered to do one on mine.
Hope that helps.