I don't have a GAHH glass top, but did transplant a factory 03 glass top and frame on my car not long ago, and know that there is an adjustment for the frame in order to make it so that the top latch does not touch the windstop when you cycle the top up and down. This should be an easy fix. Take a look at the first picture in the link:
http://mike.focke.googlepages.com/removingthetopandframe
Here, you will see 2 of the 3 bolts you will need to loosen on each side of the top frame. They are circled in red. There is a 3rd bolt right above the bolt on the top of the picture. Just loosen those bolts (don't remove them), and then have someone pull the frame rearward as much as they can while you retighten the 3 bolts. If you have that little screw that has a blue arrow pointing to it (there's actually 2 of those, but you can't see the other one in that picture, as it sits further back), you will have to loosen these too (some top frames don't have these screws there). This will prevent the top latch hook from touching the windstop.
As for the engine access issue, you can fabricate your own strap to increase the engine access on your aftermarket top. Take a look at the strap that the Robbins glass top maker fabricated and includes with all their aftermarket glass tops. Since their glass window tops are installed on the older 3-bow frames, they won't fully pivot out of the way like the factory 03+ top frames allow, but fabricating this makeshift strap will effectively pull the glass window away from the engine cover, and get you the access you need to service the engine from the top.
