Time to give up on the Thermoquad?

Not following. That wont fit the well, will it? You just want to be able to run a Holley jet,

It won't? LOL, are you sure ??????
Yes, run the easy to get Holley jet.

and not having the well in the way makes it possible to do the mod, correct? Would you still run the metering rod?

Correct. Otherwise, at least for now, not that I have looked for it, the tap is tappered. I would need a bottoming out tap (Flat, not tappered) to do the work. Then flip the carb base over and get all the shavings out.

I'd rather the well bottom gone myself to do the work.

Yes, run a metering rod. The rod set is adjustable in height on a TQ. So extra jet height is not an issue. (Same if the jet is shorter. Adjust the rods downward.)