Hey, I did some tests and I'm pretty sure that there wont be any wind noise from the handles. I don't care too much if there is, as the car will be noisy anyways.
As for the seat brace on the pan, you can kinda see what I'v done here.
Nothing from the old system is left on my car.
The plate you can see in the picture is welded to the brace which runs in the channel where the body mounts. The body now mounts through the brace. I beleave I have seen products offered which are similar but I did mine almost 8 years ago when I was doing the pan.