I did this same job late last week - completely disassembled hard top for paint in the spring. Ran with a bikini top all summer. It is a major pain. I also insulated the roof and did the headliner.
Couple tips -
- Lightly tack the big roof seal to the top around all the holes so the rubber isn't an issue lining up the holes for the bolts. (I did this)
- Glue the rubber flat "packing" piece w/ the holes to the hardtop sides (not the tub). (I didn't do this but it would have helped.)
- Using blue painters tape hold the side rail "lip" molding down. There's enough room to pull the tape out later. I had the seal pop out at the rear tub corners a couple times after setting the sides on while trying to get everything else lined up. It's a real pain trying to remedy once more pieces are bolted up.
- Bolt the sides on LOOSELY. You'll need the flexibility.
- The rear crossbar is a real pain - do that first while you have plenty of slack in other areas. There are two bolts that attach the bar to the sides that should be started before the top is set on. The heads will protrude through larger holes in the rain gutter metal. The small pieces of weatherstripping for this area will need holes punched for these bolts. (The slots already cut are for the next outward bolt hole). Work on the corner brackets and these bolts simultaneously until everything is loosely bolted up.
- Tape the outer corners of the windshield top seal down. Hard to line up otherwise.
- Set the hardtop on - WITH help. Before setting it in place I used thick Polyethylene tape on the front metal edge of the hardtop roof to protect the paint on the windshield frame. (Amazon link https://www.amazon.com/gp/product/B00823JDRS/). You will have to shift things around a bit and I was paranoid about scratching something. (I used this stuff in a lot of areas like the hinges, bib, side panels, running boards, etc to protect two painted surfaces and eliminate squeeks. It's good stuff available in different width/thickness).
- The bolts that go DOWN from the hardtop to the rear x-member should be next. These are the only "blind" bolts that go down and are the hardest to get started.
- Loosely bolt up the door crossbars next. Be careful here as the scratch potential is high - especially at the windshield.
- Start the two bolts at front of windshield.
- Get the rest of the top bolts started.
- You can remove the blue tape holding the tub lip molding down. Pulled out from both sides easily.
- I then alternated tightening everything up from side to side and upper/lower gradually working around. I suspect after the rubber settles in a week or two I'll have to repeat.
I decided to have a pro install the side and corner glass and then I'll be done. I sure hope removing and installing the top in one piece is easier next year. If not...I'm adding A/C!