It takes a big man to admit his mistakes... Yesterday I became a big man.
Since I installed the rockers a few weeks ago, I have been looking at the alignment with the inner heater channel and the channel on the floor pan. There was about a 1/4" offset from the pan channel to the edge of the inner heater channel. On the passenger side (still original) the pan and heater channels line up with maybe 1/16" offset, but closer to none.
That said, I decided to cut the heater channel loose and move it toward the inside. It took about an hour to cut all the welds loose and remove the dog leg. After I did, I couldn't get the channel over more than about 1/16". Not enough to make a difference. I went under the car to find out what was holding the channel up and it was the outer lip of the pans. I had a spot near the jack area that was not trimmed far enough. I trimmed it down and the channel freed up to move further in... Then there are flutes in the heater channel (where water is supposed to drain) that were hitting the pan, so I carved out recesses where those where and the channel was freed up to move even further in. I went back topside and clamped everything where I wanted it and tacked it in to make sure everything looks lined up. I am MUCH happier with the channels now. I will re-attach the dog leg and firm everything up today.
Now that you have heard my personal growth story, it's time to get back in the garage!!!