I'm having similar issues with my top. I resolved the problem with the top not reaching the window frame by lengthening the push rods. I'm having other issues though. Boxstaboy referred me to his his partner Maurice and I have pasted a copy of our e-mail correspondence below in the event it can help you. I'm waiting for my nephew to have some free time to help with my adjustment. I think I'm in for an hour or two of trial and error.
My e-mail to Maurice:
Thanks for responding. I really appreciate your pioneering work on the 03/04 top retrofit. I’m basically successful, but I have a few minor issues to address.
1. The hook on the top latch bumps the wind stop when it goes past it. I have addressed this by closing the latch when it is in transit. I did not have to do that on my original top, and I checked a friend’s 04 with the original top and his latch hook clears the wind stop without closing it.
2. The clamshell won’t close completely when the top is in the down or open position. It closes fine when the top is in the up or closed position. It’s as if the top is stacking too high. I can press the clamshell closed with my hand, but again that doesn’t seem right.
3. The area of the top behind the b-pillar area seems to be developing an area where something is poking into it when it is down. I’m a little concerned that this could cause a wear spot that eventually leads to a hole.
4. When the top is moving towards the windshield header, it suddenly moves forward and drops the last 3-4 inches. My old top closed more slowly and there was no sudden lurching at the end.
You can see some pictures in this post on the 986 Forum:
http://986forum.com/forums/general-discussions/33406-glass-top-install-question.html
I’ve aligned the back of the top (where it meets the clamshell when it is in the closed position) so that it looks like my friends 04. I originally tried lowering the rear edge a bit. That made the clamshell fit better, but this let water in when I washed the car.
I’d appreciate any suggestions for fixing these glitches.
Maurice's response:
1. To get the top latch to clear the bump stop, you have to first loosen the three bolts on each side of the base ( and remove any Phillips screws that you may find on those brackets, some have one, some have two, and some have none). Now, pull back on one of the brackets and tighten one of the bolts on that side. Do the same on the other side and then tighten the other two bolts on each side. You won't feel much movement, but there is just enough play that, if you get it pulled back hard enough and don't let it go back forward before you tighten the first bolt, the latch hook will just clear the plexiglass windscreen. It helps if you have another guy pushing back on the base of the B-pillar bracket, but it is possible to do it by yourself. There has been only one occasion where we had to elongate the holes very slightly to get the clearance, but that was a fluke.
2. Double check that there is nothing in the convertible top well that might interfere with the proper folding of the top and that the top liner is fastened correctly at all of its clips. Also, lubricate the mechanism with a white lithium grease spray (or Dupont Krytox if you don't mind spending the $$). Then, also try tightening the rear main bow downwards by one turn at a time on those adjusting brackets. You will find the bracket by following each tension rope down from the underside of the rear main bow. It's a 14mm bolt head and you turn it CCW to get it to pull the rear main bow down a little further.
3. Is this happening evenly on both sides or is one side bad and the other side okay?
4. The cause of the lurching is either that one of your plastic ball cups has popped off its steel ball or there is a lack of lubrication on the black plastic sliders that ride back and forth on the rails that are located horizontally a few inches below the top surface of the rear quarter panel, on the inboard side of the quarter panel. If you follow the body-colored support arm of the clamshell you will find the black plastic slider into which a steel ball from the base of the support arm is pressed in. Sometimes one of the black plastic sliders is worn and it either wobbles inside the channel or the steel ball pops out, sometimes it's just a matter of lubricating the channel with white lithium grease.
Let me know how you make out and if I can be of further help.
Regards, Maurice.