Back about a zillion years ago, when Holley first started talking about EFI, I was writing for Super Ford Magazine. I called Holley and asked if they'd given any thought to doing a package for factory dual quads. They first told me that it'd be six months before they went to dual quads, and after several months they'd decided not to do it at all, "For the forseeable future."
I told them I had a car to work on---Brother Lon's '67 Mustang with 427 TP engine---and offered to do all the work if they'd help me with the tech stuff. We agreed, and over a few weeks, installed two complete systems, with separate electronics, but a single paired fuel delivery system. I won't go through the whole scenario, but we did put together the very first dual system that Holley was aware of. By the way, it worked great when we got it all sorted out. I wrote several articles for Super Ford as we did the work, and Lon's car was on the cover when we wrapped it all up.
Now, to your proposed project. First, throttle body EFI systems that have the injectors mounted in the throttle bodies are set up in such a way, that all four injectors run all the time. They are not staged, with primary and secondary barrels like a carb has. Therefore, with two throttle bodies, you'll have one injector for each cylinder, and all eight will run all the time. There will be no imbalance if you were to mount the TBs sideways.
Don't expect to be able to switch to methanol and use the original TB injectors. Methanol is a wonderful competition fuel. It's much more desirable than gasoline. But stoichiometric values for gasoline are about 12.5/1 if you are looking for greatest performance (14.5/1 for driving down the street). The equivalent performance value for methanol is more like 4/1. Very likely injectors for TBI aren't available that are that large, and the system isn't designed with enough tuning latitude to work. Drag-'n'-drive engines such as are used in Drag Week have a completely separate set of eight njectors for the 'drive' activity on gasoline, and use sixteen much larger injectors to provide the methanol for the 'drag' activity.
For what it's worth, I'll never use carburetors again. EFI opens up a whole new world of performance.
KS