[DannoXYZ]

I re-read OP's post and issue appeared after adjusting bodywork. Perhaps wiring got crimped or vacuum-line got pulled and disconnected. Rather than backtracking and finding which went wrong, multiple parts-replacement ensued which introduced numerous possible errors into system. I recommend putting ALL original parts back on bike, except for perhaps IG-switch & ECU since hot-wiring ignition-switch may be bit too advanced at this stage.

Also my first suggestion is to get factory workshop manual for this bike. Professional dealer mechanics consult manual for many reasons. Mainly to save tonnes of money and tonnes of time. They will often spend some time with measurements and troubleshooting to arrive at diagnosis and replace just single part that is confirmed bad. Not shotgunning pile of random parts at bike hoping it'll hit something.

My second suggestion is to get multimeter and learn to use it to measure voltage and resistance (perhaps also current). Most of diagnostic tests in manual involve measuring these properties of engine's parts and systems to determine what's good and what's bad. There's plenty of YouTube videos that shows how to measure these things. Such as this:

Link to original page on YouTube.

There's absolutely ZERO, NONE, NADA, ZILCH chance that you're gonna be able to properly follow manual and determine what's wrong without knowing how to use multimeter proficiently. For over 100-years, mechanic's most valuable tools have been multimeter and vacuum-gauge. Nowdays, many diagnostic steps can be combined and redundancy reduced if you also know how to use oscilloscope.

Originally Posted by Clockwork Orange

2. My test on the fuel pump was by taking the tank off and connected a spare battery to it to check that it was pumping fuel at a good rate. I have no idea how to measure this or any of the other sensors as described above.

Ok, this is flow test not pressure test. Both require instruments to measure and arrive at numbers. These numbers depending upon what they are, will tell you if part's properties are good or bad and needing replacement. Not sure how you arrived at "It seems to be getting sufficient fuel." or "I have checked the pressure from the fuel pump and its good." without any instrumented testing and examining numbers.

Pressure is measured by gauge which presents data as force per unit area, such as psi, or bar or kPa. Similar to tyre-pressure gauge, but for fuel-lines. You can squeeze tyre and say, "yes, there's pressure alright", but without instrumented testing with numbers, you have no idea what actual pressure is. Many people have died because of using tyre-pressure outside of bike manufacturer's recommended range. Without gauge reading out actual numbers, you have no idea if pressure is within safe-range.

What you actually tested was flow-rate, and you need to measure that. Flow is typically represented by volume per unit time. In this case, aim fuel-hose into measuring-cup and run fuel-pump for 3-seconds (use stopwatch). How much petrol (milli-litres) did you collect in 3-seconds? Multiply that number by 20 and we get flow-rate in milli-litres per minute (ml/min).

3. I was told that the clicking sound could be a sub throttle sensor so I replaced the throttle bodies as I believe these sensors are sset in the factory and cant just be replaced.

Nope, they are adjustable and sensor never goes bad. It's activator motor that needs to be adjusted and that clicking sound is mis-adjusted motor. It's banging into end-of-travel of valve and hurting itself.

Most likely, it's TPS-sensor that's out of adjustment first. Idle-switch on TPS is probably not contacting properly due to incorrect angle-adjustment on TPS. So ECU is trying to adjust sub-throttles to compensate because it doesn't know that throttle is closed. Brand-new out-of-factory throttle-bodies need to have TPS and sub-throttle sensors adjusted before use. Procedure is in manual and requires use of multimeter.

At this point, put original throttle-bodies back in. Most likely those were adjusted properly and removes one additional error-point that's in system now.

4. As per a link I was sent I checked for error codes on the FI light and found 4 errors:
a) 1 long 1 short - Main throttle sensor

Yup, you changed throttle-bodies without properly measuring TPS and adjusting to factory specs.

b) 1 long 2 short - Inlet air pressure sensor

MAP sensor. Needs testing to determine if it's reporting proper manifold-pressure. Verification is mechanically measuring actual engine vacuum, and seeing if sensor's output-voltage is proper for those conditions. For example, with key-ON and engine OFF, MAP-sensor should be measuring atmospheric pressure ~101kpa. Is it sending out proper voltage for 101kpa?

Then measure vacuum at idle, should be ~30-35kpa, but what is actual vacuum you measured? Is MAP-sensor sending out proper voltage for that manifold pressure? Having secondary measurement (mechanical vacuum) lets you verify and test if electronic measurement (MAP sensor) is correct. If not, then you replace sensor knowing for sure it's bad. Or if you measured non-standard vacuum, then you've got vacuum-leak somewhere that's tricking MAP-sensor into sending erroneous data to ECU. This is more likely the case than bad MAP-sensor (they're very simple and robust sensors).

c) 3 long 1 short - Vehicle down sensor
d) 3 long 2 short - Sub throttle sensor

I dont know if these are old codes that need to be reset or if these are current problems.

The answer to that OR is to measure those sensors and determine if they are sending out correct output voltage for conditions. Once you've verified sensors are sending out proper voltage for conditions, THEN you reset codes.

It's like having "bulb burnt-out" error code. You can keep on resetting that code and it goes away for bit, then it comes right back again. You reset it and it comes back again. At some point, you need to look at bulb and see that it's actually burnt out. Then replace it. Or find broken wiring and fix that. Code is symptom (effect), not actual problem (cause). Fix problem and symptoms will automatically go away.

How could all these things go at once??

Because you changed systems that incorporate them. Those parts themselves aren't bad, but are connected to systems that may be malfunctioning due to improper adjustments. Backtrack and undo your changes and put system back to original condition before fiddling with bodywork.

BTW - those error codes you got, was it from Dealer Mode 1 test or Dealer Mode 2?