Update
So this operation was somewhat interrupted by a broken bracket for my power steering ram cylinder.
When the bracket broke, I'd just discovered that the driver's side cowl was suffering from worse collateral damage than the passenger's. Again there were holes from an errant air chisel, but the complications came from much more welding detritus in the area and the major damage being behind the drain hole rather than directly accessible as with the passenger side which I bent back into rough shape.
Without the broken bracket, I might have tried to plug the holes with seam sealer and/or the JB product. After all, the car rarely gets wet other than the times I wash it. But it's funny how a seemingly non-related issue can put another over the top.
"Why?" you ask. Because the bracket was welded on and any solution was going to involve additional welding. Since my landlord's garage with the natural gas lines running overhead did not strike me as the best place to teach myself to weld, back the local Mustang shop the car went. Once it was there and I was paying for their awe-inspiring welder's work, it was worth it to me to dispense with the issue once and for all, especially since I was tired of messing around with the subpar workmanship from the earlier body work (a now out of business shop in Texas).
We went with a version of the "tin can" option. Generally this approach cuts the upper cowl in the area below the fenders and peels it back so that the repair work is minimally visible when the car is reassembled. Because we strongly suspected that there was damage under an area that might generally be obscured by peeling the metal back, the guys and the shop drilled out the spot welds to take the ends of the upper cowl completely off.
Here's a shot of the basic approach.
Here is what they found on the driver's side.
And here is another.
And here is a shot of the passenger's side removed with some of the damaged sheet metal removed in preparation for repair.
That last picture is not the best but it also shows the hole on the side panel caused by misalignment of things in the earlier body work.
As you may be able to see from the pictures, the shop is resealing the hats, they are patching the holes, and they will also be treating the cowl gutters with a rust sealing paint so that if anyone has to deal with this again it will -- the good Lord willing and the creek don't rise -- be my kid.
Although the side panels are incorrect for '67 since the earlier panels were all that was available when the initial work was done and the passenger side will need to be patched, I'm planning on leaving this be since the stamping pattern on the steel is not important enough to me to tear the two sides out without a bigger problem.
Perhaps I can finally put in the new carpet, which is the weekend project I thought I was starting, and button things up properly.