To follow up on this install....
After driving around for a bit I found the Magnaflow install has pulled the exhaust lower and it was up against the rear edge of the tunnel brace. So I went to Lowes and bought longer bolts and a couple boxes of washers. I think it took seven washers on each bolt to get it low enough.
There may be better solutions, but this was simple and cheap.
As far as gas milage goes over time I have seen no real change. I have not replicated that first trip. My car must have been running a bit lean and now the computer has things right back to where they were before the install.
Also the performance is back too. Power shifting into second now brings on the traction control big time. I should really get out to the track to see what it will do.
Now the bad. Drone. It is there. My first rides were with the windows were down and I did not notice the dreaded drone. Now that the weather is cooler and the windows are up the drone is noticeable. The other day I was out with three passengers and the drone was pretty bad. in sixth gear from 50-70 and especially bad going uphill.
Shifting down to fifth is better. With just me in the car it is not quite as bad, but still there.
So what next? Maybe the Helmholtz solution. Or maybe some gears. I still have the LS3 resonators on, maybe they are the culprit.