I think that I bent the rail before drilling the holes through the spacer and the bending was done in a vise with the parts separated, a little bit at a time.
If you mark with a felt pen where the bend line should be on the rail and then separate the pieces you should still be able to bend the parts to match. It is an iterative process.
Thanks, I used a vise with a large wood dowel and forced it by hand. Marking the radius on the rail was a good idea. After several small bends it came out OK.
I may be a little late with my comment now that you have drilled to 2 rivet hole, but...
The most important part is that it lay flat against the longer portion of the rail. The gap seal only slides on that portion. It doesn't go around the corner. The curved portion of the track is covered mostly by the aft skirt so even if you need to tap it with a hammer to get the shape that you want it should be fine. The upper most portion won't be visible.