Dan - I wound up taking out about ¾" from the main bow and ⅞" from the rear bow (at the center of each) for the best fit on my top. Fortunately, I didn't need to modify any other parts except for installing larger screws for the top latch hooks on the windshield posts, as previously described.
On a side note, I installed a Sunbeam Tiger shift boot a year ago which solved all of my "popping out of gear" problems. This topic has been dealt with before on this forum, but here is a link to the vendor where I bought mine:
http://www.rootes.com/
If your shifting problems disappear with your current shift boot completely pulled away from the tunnel, then this solution may work for you. The Tiger shift boot is thinner and much more pliable than the ones supplied with our ERA kits (possibly other kit brands, too); it looks identical when installed. This simple change made me a happy camper.