As Steve wrote, you may be a bit low. The "missing" material is simply a thick fold of material that extends out from the inside edge of the frame about 3/8 to 1/2", depending on how TRF finishes it. Here are the things you are looking for while fitting:
1) The forward rail of the frame must be parallel to the windscreen post, and leave about 1/2" measured from the frame into and fully forward within the slot in the windscreen post. This is the MOST important measurement during the fitting, as that material fitting into the slot stops water from blowing directly in your face.
2) The top rail of your frame must reach above the material flap hanging down on the inside of your top. It must reach the flap, but cannot go any higher than the edge of the outer top material. Parallel is best, but not at the cost of losing your forward frame rail alignment. Closer to the outside top material is also better for sealing.
3) Ensure the rear rail also lies on top of the inner top material flap. This is the least important fit...but it still must overlap the inner top flap material.
If you study the windscreen post and top material, you will see how they designed a sealing flap to capture the "missing" tab on your sidescreen. Once you understand how the seal works, you can best align the frame to optimize sealing. Remember, the priority is front, then top, and finally rear fit.
The frame will be fit at TRF to match the acetate windows, so they may alter the angle of the frame slightly. This means you may have to adjust the fit after the rebuild, but if you fit the brackets with a bare frame, it should be close enough to adjust later.
It's a fun time when you get to this stage!