Wait until others with real experience answer but I'll tell you what I think, that factory spacing to the second to the last bow is the most important measurement. Do you have the new top? Put your rear bows spacers like they have in the GM manual, measure it off perfectly and set it up like they want. Don't put the rear curtain on just yet, first lay the top over the irons and see how it fits up to the rails at the quarter windows. Now go under the and look at that loop of material that mounts the top to the second from the front bow. There is a piece of metal that is screwed to that second to the front bow. The strip of metal goes thru that loop of material and then you slip it into that bow and put the screws from underneath. If you removed the old top you know this of course. But check it out, when that top is in place like this your rear bow height should be right there under the seam on the ends of the rear valance. There is VERY little room for error. I couldn't understand why everyone was making such a big deal about that bow height. I just couldn't understand why if that bow was forward or rearward an inch or so what the big deal would be. LOL, HOLY COW was I wrong and found out real quick when I put that top on for the first time! The top doesn't have much movement, you are SCREWED if that bow is in the wrong place.
But lay it out, look at it, I don't understand why that bow height off the rear moulding is that big of a deal, the distance between the rear bow and the second to the last bow is REALLY where the rubber meets the road. THAT is your top, your irons, that rear bow distance to the second to the rear bow IS your top. That is where the top mounts and at the rear of the curtain to the body is darn near irrelevant. At least that's how I see it, but let some others give you their thoughts.