It is hard to get an accurate measurement from the Jeep door opening, IMO a better way to measure is from the tub seam where the front fenders /hood meet the tub, i.e. about 12" in front of the windshield and door openings. From this seam to the farthest rear opening is 117 3/16". You keep the body square and build to this and you will be A-OK.
To get to 117 and 3/16" this is approx a 10" stretch in front of the wheel well (wheelbase) and about 14" behind the wheel well or there about...
After doing what you are attempting I realize a hard top is difficult to move on and off for taking measurements, a easier way would be to get ahold of a set of bestop soft top rails and use them for alignment on each side.
As for the full length hard top... I looked for a while, could not find a good one for under $1,000 and once you figure travel-- Just buy a new one for an extra $700, then you do not mess with 20+ year old fiberglass, missing hardware, the wrong color...