The raising of the passenger side inner fender went faster now that I had an idea where to cut and what to do. After everything was welded up on both sides I went ahead and sprayed the "fixed" areas with spray bedliner in a can, since that's apparently what one of the previous owners of this rig already did. I was impressed how well it blended in.
I did take the time to measure the "virtual lift" and both inner fenders were raised exactly two inches. I probably could have pushed it another inch, but there would have been several other clearance issues I'd have to deal with. At two inches I have just enough room to make everything work.
Here is a shot of the drivers side, you can see the stainless header is now installed. I had to add about 6 inches to the O2 sensor wire.