*cough* Replace the bike with anything else ...
Seriously, the tuner that you describe is only an EFI calibration instrument. That cannot change the amount of air that the engine draws in. The amount of air that the engine draws in, is established by the "hard parts" ... camshaft, intake port and runner configuration, exhaust port configuration, etc.
And, VE is not a single number. It's one thing to get good VE at low revs. It's quite another to get it at high (for that engine ...) revs. The things that are needed to get good VE at high revs are quite likely to result in poor VE at low revs, so one needs to find an appropriate balance between the two, depending on what the engine is being used for. Intake runners that are tuned for harmonic resonance will add to VE at specific RPM points but equally take it away at other points. Again, the objective has to be changed depending on what you will be doing with the engine. Drag racers don't care about VE at 1500 rpm. Cross-country tourers normally don't care about VE at 6500 rpm or whatever your redline is. So, what's the objective?
The specifics of what needs to be done, you'll have to ask a H-D specialist. From my perspective, the engine configuration is all wrong (V-angle is too narrow, it's poorly balanced and prevents a good bore/stroke ratio from being used and that prevents high revs), the intake port configuration is all wrong, the valvetrain is all wrong, the cooling system is all wrong. Start over, with something having a wider V-angle (ideally 90 degrees so that no balance shaft is needed), wider bore shorter stroke, move the camshafts up to the head, use 4 valves per cylinder with a pentroof chamber and a shallow included angle, add liquid cooling, add individual tuned-length intake runners, and sort out the exhaust ... i.e. get a Ducati.