I was pressed for time this summer, and took my car into an upholstery shop to get my new top installed. The windshield was not installed when I bought my car, and it had no top. I explained the problem in lining things up, and the gentleman said he thought he could correct this. He had seen frames pulled back from heavy drivers pulling on it to get out of the car on TR6's before, and was confident he could line up the windshield and windows. He did a great job installing the top, but not much better than me in lining things up. He said that it couldn't be off more than 3/4", that he could still install the top with no ill effects later with minor adjustments. He said I could try bringing it back in after my trip and could try again. So, to make a long story short, yes, I can get the latch pins in. When I roll up the side windows, the top of the window rubs the windshield frame. Sorry for my long winded answer. I wish I could locate a local TR6 to compare, but my engine is torn down at the moment.
Kevin