When I did mine I used a cutting wheel on the LH side. I ran out of time before the Windrock trip and so I drove it there half done. When I got to the hotel parking lot, the first thing I did was whip out the sawzall and cut off the RH side. By far the sawzall was easier and quicker. I picked a start at the base of the seam where it comes together and just followed what I thought the tire arc would be and zipped it off. I had already cut my rails prior so it was easy to do. I followed up the rough cut with a file smoothing. Probably not required but I didn't want to have sharp metal hanging around to gash myself on I next time I'm working around the area. Then I hit it with brake cleaner and a rag and put a coat of Rustoleum satin black on it.
This pic is prior to the cut but shows roughly the line I took. I don't know that I even needed to trim with just 35s but I eventually will run 37s so the work is done.
It should be noted that I smoked the insulation between the sheet metal with the cutting wheel. Freaked me out a bit. Thought I might start my rig ablaze but it didn't happen. Someone suggested using JB Weld to fill the gap but I didn't since the gap was already open to the elements prior to the cut anyway. But just something to think about. Might be an ok idea.
Hope this helped.