It looks like the tear is above the hinge? Looks like the material just got pinched and sheared?
IMO the rear bow height would not really matter, as the binding is far forward and the only real difference in the bow moving an inch or so is cosmetic and where the glass sits in the opening (when installing my 68 years ago the initial install pulled the rear bow down about an inch due to side pad stretch. The top worked fine, but the shift made the rear pads loose, so has to remove and refit. So do not think minor variaition here has any major impact on operation). And once the top starts going up the rear area folds and there is no strain from there applied forward to the area over the hinge when lowering the top.
How far did you disassemble the frame? Did you remove the side links and replace, or just remove the bows? They really are not that complex, a bit fiddly with the nut/washer/bolt orientation and assembly order, but the parts really only go together one way (you can install the balance links backwards though, but that binds quickly and is very evident). Photos of the assembly before the top went on?
Unsure why the stitching noted would be any issue The area between bow 2 and the header is partly glued to the front side rail between bow 2 and the header, and seem far forward of the damaged area. Can not see how that would impact the fold between bow 2 and 3.
If you removed and reinstalled the side links, do you have photos? Hard to get them wrong, but that is the first thing I would look at for if they may be binding or pinching when getting to full lowered position. Here is a picture of a 68 top showing the orientation of the main hinge to rear side link. Suggest raising the top 1/3 to 1/2 and inspecting the action of the hinges, bows and side links to see if the area of bind can be found. Then slowly go further looking at how the top kinematics go and how the fabric behaves. Compare side-to-side to look for differences. Post more info.
In comparing the EZ-On to Robbins and Kee side-by-side I found a few slight differences, but nothing of note that led me to favour one over the other construction wise. Can not speak to how "factory accurate" they are (none probably are) but the EZ-On does come with the brass zipper, a reason I'd recommend it over the others. All I looked at measured up very similar and did not see anything that would impact the fold in this area, construction wise. Minor variations in stitching and the fabrication and "rain flaps" in the side wells.
The stitching shown does look odd. I can unbox my EZ-on "test top" and compare to your photo if you like. It may be a fabrication defect. But I'm not sure the sewn pocket would make much difference as the cable is only connected at the two ends, the pocket is jut a keeper along the lower edge to reduce flapping in the wind and isn't really a binding point as I can see. I'd suggest that maybe the glued flap along the front side rail is more likely an "possible", how far back down the frame does it go? Mine stops about halfway between bow 2 and the header, if further back it may have an impact.
Lastly, what year top frame is it? They do differ slightly and while it is basically the same there may be a variant depending on the year that could be impacting the issue. Unlikely, but happy to compare the 5 "assessment frames" I have (65, 66, 67, 68 and Dynacorn) to see if I can help spot anything that could be a cause.
Post more info, interesting (if disappointing) issue...
