Instead of writing up a full instructional manual which some other have already done nicely on the web, I'll just give some tips from my own experience below to make things easier for installation. If you find some redundancies or discrepancies in my instructions/tips below, please use your own judgement..
Before starting the job, plan ahead to have a free full-day. It takes 2 people 6-10 hours straight. Ten-hour is my worst case where I had to put back my softtop from winter (weight saving) and I had to trim quite a bit of metal out of the seat beat towers. It's good to have a 2nd car available if you have to go out in the middle of the job to buy some tools or lunch. Make sure you have enough space in a flat garage to prepare for taking the hardtop on and off. For tools, you need:
- 2 good jack stands and a floor jack for the diff housing,
- Dremel with cut-off wheels,
- automatic punch or what-have-you for marking pilot holes,
- power drill and 2 drill bits, a 1/16" or what-have-you for
piloting and the "full-size" bit (unfortunately I've
forgotten the size since it's been a year and I'm too lazy to
find out, but for sure you don't need a long bit)
- Ratchet and sockets, wrenches, Phillips screwdriver for
removing plastic covers inside wheel well,
- scissors to trim carpet,
- pliers to ply off plastic caps on the carpet,
- vacuum cleaner.
Step 1: Remove everything to prepare for test-fitting
Remove anything in the way to prepare for test-fitting. That
should include hardtop, seats, side trim panels, seat-belt tower
bolts, seat-belt reels, parcel shelf cover plate under the
carpet.
Step 2: Trim the parcel-shelf to clear the rear bars
Trim with the dremel. It's easiest to make 2 90-deg cuts for each
side. The other 2 sets of 2 90-deg cuts should be on the cover
side that make up the square "holes". My bar is a tiny
bit different than Terence's later revision. So it's hard to say
where to cut.
Step 3: Test fit the bar
Put the bar in. Thread on the 2 nuts to go with the bolts welded
into the bar. IMPORTANT! The bar should have free-play sideways.
Try to get each rear bar endplate as even to the chassis-weld as
possible. If an endplate is too close to the center line of the
car, you'll have a hard time to put on the backing plate and nuts
underneath the car. Tighten down the 2 nuts. Check to see if the
holes on the vertical plates matches the holes on the seat-belt
tower wall. If not, mark the part of the seat-belt tower wall to
be trimmed. Test bar clearance with softtop and hardtop. It's
difficult to see clearance between bar top and hardtop interior.
Use a piece of cloth to test clearance. In my case, the front bar
was too tall so I had to spend the following hour or so to trim
metal off my seat-belt towers!
Step 4: Drill pilot holes
Use an automatic punch to mark positions for rear endplate bolts.
Remove bar. Drill the 6 pilot holes.
Step 5: Drill the holes
Despite what others say about using a long drill bit, I drilled
from underneath the car. Jack up the car from the diff housing.
Put on jack stands at the factory scissor-jack points for
changing rear tires. Remove wheels. Remove plastic covers inside
wheel well to reveal pilot holes. It sounds impossible to drill
thru' chassis but it you have a brand new drill bit, you'll be
amazed by how easy you can drill thru'. Put on some
eye-protection as dirt/debris flies off.
Step 6: Put the bar in
While the bar is out and seat-belt towers have been trimmed if
necessary, stack up the seat-belt tower spacers to flush with the
front endplates. While some may recommend not putting the spacers
in at all, I think it's an added security. Trimming on the
spacers may be necessary and don't leave any free-play or you'll
hear clinking sound later on.
Put in the bar as close to the previous position as possible. Put on seat belt posts. Thread on all bolts and nuts. Remember to put the backing plates underneath the car before putting on the nuts. Tighten the nuts on the weld-in bolts 1st, then the factory seat-belt tower bolts, forward-facing bolt, and finally the bolts on the rear endplates. Put back the seat belt reels.
Some may recommend jacking the diff to make sure the chassis was not twisted from one side to the other before tightening the bolts. But I left the jack stands at the aforementioned jack points to have as much pushing force acting from the rear bar to the rear shock tower as possible.
Step 7: Put things back and clean up Put back plastic covers and wheels. Lower the car onto ground. Use your own creativity to trim the deck cover, side trim panels, and carpets. :-) Put them back, clean up and put back the seats.
Step 8: Final testing
Test drive with soft top up, then hardtop up (even if it looks
stupid to drive with a hardtop in the summer). Make sure no
scratching, clinking noise, etc..
Next: 
Mutilated and
hand-polished valve cover