Battery is new and voltage is perfect off and when fuel pump is priming - This does not actually cause me any issues, it just primes continuously and im not sure if thats dangerous at all.
I'm not sure if it is dangerous, but it is a bit puzzling. As far as I know, the ECU controls power to the fuel pump, via the Y/B lead, which grounds the fuel pump relay. It also monitors the output line of the relay, which powers the pump, via the Y/R lead (see diagram on page 4-83 of the manual). If the fuel pump is getting power, even though the ECU isn't trying to power it, by grounding the relay, a C41 should be thrown. As far as I know the ECU doesn't command the fuel pump to stay on all the time, until the engine has started, so I would expect a code, which you say is not the case...
NO flickering - I literally have the line central and the code with red light on ( -- c29 ) When I first turn on the ignition in dealer mode, the line line is at the bottom but quickly moves up but I think thats just related to it getting the reading as it stays central.
If the dash is in the middle with the engine not running, then it's probably set too low, but that's unlikely to be related to your current problems, so leave it for now.
I dont recall the old Throttle body making a clicking noise when the butterflies open/close on start up - this leads me to believe it must be out of position on the new throttle body ? sounds right?
As far as I can tell, the secondary plates will click a couple of times, even with the STPS properly set. This is likely a means of calibrating the servo on each startup, by having them bang against the upper stop, to find out where it is. In any case, it shouldn't click for long and it shouldn't throw a code afterwards, so if it does, then that would make a maladjusted STPS more likely, as you suspect.
Also - would this really cause a WOT problem ? not that I like doing it often but when I tried revving in neutral it does red line - does this indicate anything to anyone? hopefully more fuel delivery related (kink in hose) rather than butterflies ?
Since the secondary plates are placed just upstream of the primaries in the intake tracts, they essentially behave like an overriding throttle, i.e. even if you go WOT, if the secondaries open only half-way, it's more or less as if you had opened the throttle half-way. So yes, they can cause all sorts of problems, depending on the specifics of the mode of failure: if they behave consistently, but open only part way, they will have the same effect, as if you'd replaced your throttle tube with one with a smaller cam, so that going WOT on the grip, doesn't open the throttle all the way (that is, more or less like a properly operating smaller displacement engine), If they behave erratically, the engine's overall throttling will behave erratically, which is not a great situation to be in.
Finally redlining in neutral doesn't say much, since you need way less than WOT to reach the redline in neutral.