Yes, the secondary throttle has a position sensor and yes, it will generate an error if it cannot reach the position the ECU places it.
It is unlikely that a plugged vent would cause such severe fuel starvation because as already mentioned, the fuel pump would just crush the tank and keep going. But as you mentioned, a super-easy test is to ride the bike around with the fuel cap cracked and see if the problem disappears.
As far as replacing the fuel pump and screen, what was it replace with? Something uses I suspect. And if that pump were not taken apart, it is entirely probable that a clogged screen was exchanged for a different but still clogged screen. Not likely perhaps but possible.
It could be clogged fuel injectors but man would they have to be uber- clogged to actually stop the engine from producing even 1/4 of its potential power. Fuel injectors generally fail in two ways, neither of which will actually prevent the engine from running <reasonably> close to normal, at least at first glance. The two failure modes are 1) leaking injectors which are not much of a problem at speed and under load (more of an idle / starting problem) and 2) a dirty injector nozzle(s) that do not spray fuel but instead squirt a stream of fuel into the intake. Again, the engine will run, and fairly close to normal but low end smoothness, fuel economy, and overall running quality, especially at low throttle openings, suffers.
If the fuel pump, screen and pressure regulator have been changed, I would next give the pump assembly a volume and pressure test. Both are easy although the pressure test requires a relatively cheap gauge.
Brian
My thought exactly based on that description he just made.
But he says he replaced the pump and screen (which I assume means the filter was checked too). I suppose it could STILL have a clog. Maybe something in the lines? Hmm. His thoughts on the secondary throttles (butterflies) do kinda fit the symptoms, but I thought that would throw an error- doesn't the bike have a sensor to tell it how open they are?