Need frame rail for passenger side top $ paid

I doubt you will ever find a clean frame rail, especially after removal. The much easier, cheaper, and faster way would be to fab up new frame rails and weld them in.

will welding affect the structural integrity? what thickness of steel to use? the portion of rail is from the passengers toe to a few inches past the battery box..

Welding won't affect it....... if done properly!! If done properly it could be better than stock. If you are removing large sections of the frame it could twist or bend before you got a new section installed. If you don't know what you are doing, Stop!!!! I welded a T-top roof on my 79 slick-top, I had to; Brace the bottom so it couldn't sag, and weld in temporary braces on the inside so it would fold in or sprawl out. You have to be super careful with uni-body cars, unless you like riding around with no doors, because they will no longer close!!