I know its something that can drive one mad, I must have been lucky to get mine sorted............. after revisiting the thread it does seem there could be a number of causes all related to tension on the roof, I'm pretty sure I had the awning on open so no tension but I like that locating block that toadskin did, it should work well made of plastic like those breadboards to give a smooth durable finish, at least 50mm wide so it has a good base for adhesion and support when roof slides over it, not a tight fit to roof as some movement of roof is needed when down, I would use Sikaflez Marine adhesive as it seems to hold like the proverbial.... If you used timber then a hard wood, certainly not pine would be needed................... You would need to do some decent measuring as it may not be a case as one size block fits all with the block being to guide the roof but not hold it once down or it could get jammed.
Be a most interesting project for sure, not having a pop top now I can't do some experimenting....