Installing Replacement Top, Stumped...

Its probably because they sandwiched the rear glass between two pieces of material.

I never completely trust center markings and holes in replacement tops.

When I do tops I work from the back to the front. The rear window curtain is the first thing I put in. Mark center of the top frame and center on car with tape. Mark center of glass ( top and bottom ). Use straight edge and mark center at top and bottom flaps.

Clamp the bottom rail to the bottom flaps. You can take measurements off of the old material. I use clamps to hold the top window curtain to the top frame rail. When you stretch the bottom curtain to the studs it should be tight...but take into account the extra 1 inch. Once the top is clamped to the top frame and the bottom rail is clamped to the material, centered to the car, you can climb in the car and mark your stud locations.

I used to go to Lowes and buy all the clamps they had....kept them in good shape and returned them when I was done. I've got vice grip style clamps that I use now. Cardboard in between the jawl helps to keep from damaging the top frame or the vinyl.

Doing a top isn't an easy thing to do. If you don't have them you need stainless steel staples. Regular staples will rust out fairly quickly.