How are you going with this problem? It could be the sensor wiring connector, or the connector (for all the sensors) on the wiring loom. Possibly also the throttle body-to-main harness connectors. VFR's have quite a bit of engine vibration, which frets the connectors. Don't think that "inspecting" connectors is good enough. Fretting won't be obvious a lot of the time. You might need to learn how to unclip individual wire terminals out of the plugs, clean and re-tension them. I had a problem that kept me scratching my hea for a week and a half on my old bike (and I'm an automotive engineer). The problem was fretting wear of wires to the crank angle/cam angle sensors, but the ECU wouldn't throw the codes unless I unplugged the sensors. The same could happen with the TPS. I think you're closer to a solution than you think, but you'll have to leave no stone un-turned, and DO NOT assume that no code = ECU gets a clear signal from the sensors, because it simply isn't true.
Ok.. Finally an end to this saga. One of the sensors I replaced must have fixed the original issue. In the interim when I had the bike so disassembled, When I checked the fuel pressure with the fuel pump outside the tank, I reassembled the fuel pump/ filter I had one of the hoses clamped on the wrong side of the barb. The fuel hose blew off inside the tank and was not sending fuel to the injectors. Found that, fixed it and and now riding the wheels off of it. I am a happy camper. I love this bike. Thanks to all who helped me out on this project.