The next day I cleaned it up real good and applied seam sealer and put some primer on it. Applied seam sealer to a few areas on the tunnel along the welds used to make the tunnel higher too.
Like I said, I'll need to go back and pull the cowl out a bit to get it straight. You can see I also did not get it completely flush with the cowl, I was not going for that, I just wanted to get rid of the heater box and make it look a little better.
I don't have a picture but my Vintage Air motor had to be moved over about an inch from the original position due to fitment issues with the raised tunnel. I also welded a nut to the back of the new panel to secure the motor and it fits good now.