Points of clarification: It's TPS, Throttle Position Sensor; The 7M-GTE is paired with a KVAFM or AFM for short, Karman Vortex Air Flow Meter. The 7M-GE uses a VAFM or Vane Air Flow Meter (again AFM for short). A MAF (Mass Air Flow sensor) is a different type of device altogether... similar function just operates quite differently. (So many different devices.... such high prices for some and insane complexity with others really make me sooooo happy that there are even piggybacks out there which allow us to convert from one type of air meter to something cheaper or larger or more reliable such as a 3.5" GM MAF, GM MAP / IAT setup and so on).
The AFM did not change for any year; So unless the AFM you've installed is from a different vehicle the only thing which would cause any change is if it is in fact defective. I can't say it would be the first time I've heard of someone going through two (or five) only to find they were all bad. Now if you're referring to the Lexus 1UZ KVAFM then yes... BUT the electronic part of the assembly is still compatible, only the housings are different. The stock housing is a bit smaller than the Lex AFM. If you have a Lex and the original on hand you can install your KVAFM test it out and then swap in just the electronics from the Lex AFM and give it a go.
What I mean when I say to check E1 and E2 is for you to check all the grounds at the head of the engine. There should be one group on a separate stud on the lower part of the intake plenum and I believe another on the exhaust side by the firewall which connects to a stud by the mounts for the throttle linkage assembly... although there may only be one ground going from there to the firewall. Clean all surfaces with some sandpaper. Check the engine grounds too while you're at it; The grounds to the block and the driver's side fender.
Vc is the voltage supply for certain sensors. You should measure it at the AFM's connector and at the TPS' connector. Really if something were wrong with this line you'd most likely be seeing errors for at least the TPS and AFM (and possibly some others depending on the nature of the problem) but it's worth checking to be sure.
The TPS is a wear component which ideally should be replaced every 75K to 100K miles. As it's just a basic trim sensor a lot of them end up never being replaced and as long as the IDL switch doesn't go bad they may never get replaced during the life of the car.... That should give you a general idea of just how important they are to the vehicle's basic operation.
No there are circumstances where they may cause some significant headache such as a short across other circuits but more often even those are harness problems and not a problem in the TPS itself.