I was running today, about to get a very good time, when suddenly my FPS dropped to 30 before the final jump. It kinda ruined my run. So I did the same solution again, but with an old save, and this consistently keeps happening to me. Is this happening to you guys as well?

Yes, Moussmoose! My fps drops down to 16-20 after the part where you fly over to the connector and jammer with the box during the top of the tower. It remains that low until the run is completed. If you do the old strat where we skip spawning Samsara and Shephard, then it shouldn't lag.