If the holes are not lining up then either the side gussets(the silver metal) or the soft top bracket(the black one) is not attached to the car properly. I'm guessing someone played around with the soft top before and didn't attach them back properly.

 

is the black piece attached to anything?
My understanding was it was just attached to the silver piece and that was it.
The car did have some quarter panel repair at one time on that side.

 

I seem to have fixed my problem by adjusting the bolts in the hardtop itself several times while moving it around into the correct locations. Top now sits flush with the window sill and the latches are almost too loose, but there are no creaks/wind noise/water leaks.

Silly, I'm not sure if you have an AP1 or AP2, but you may need to bend some of that metal in to get the bolts to align if you have an AP1.

 

I have an AP1 an early 2000 before the hardtop was a option. I was going to suggest you try adjusting the hardtop latch that are attached to the top. I had no issue with my hardware on the car, after bending the ear the catches lined up perfect for me
For my final tweaking to get perfect fitment I adjusted the rear hardtop latches.

 

I attempted to mess with the latches attached to the top, but as I mentioned, the front screw on each of them seems to be loctited as it will not budge and I do not want to strip them.

 

The windshield weatherstripping on the driver side seems messed up in the one picture , is there a chunk missing from it ?.

The latches have shims under them, you can tighten them up by removing the shims under the latches, I have zero shims on mine, and they start out with 3 shims per side. Only adjust the side that needs tightening. If that doesn't tighten up enough then add washers under the front stiker plates to give you additional tightening, I actually had to add washers under the driver side striker plate to give me additional tightening even after removing all of the shims under the latch.

 

Guy I bought it from put 3 strips of weatherstripping on, it actually aligns really well.

 

Yes, the black piece is bolted to the chassis. The smaller silver part is then attached to that black part and partially to the bulkhead.

If the car had some repairs in that area, it is possible that either the repair wasn't done perfectly or the black piece could have been bent/improperly installed. How is the other side?

 

If the hook on the latch is a little loose, then put on a vinyl tube or a fuel line(3/8's I believe) on the hooks. That way the latches will grab the strikers much better and get rid of any rattling sound there may be.

You should not need any weatherstripping on the OEM top once installed properly.

 

i was able to get all 4 bolts in on the other side. I do remember reading years ago someone said not bend that piece without the bolts in because they will never line up again. I made sure the bolts were in when i bent it because of that and i still have a hole that wont line up. O well, maybe one day if i ever take the top off i will try harder with the help of someone else to move that black piece slightly so everything goes in.