RESOLVED: 3 weeks troubleshooting, still stuck

Update:
All elastomers exposed to vacuum replaced with new OE. Measured vacuum in the MAP sensor hose: Near atmospheric.
The only remaining part is the 4-way connector which I have coated with epoxy and pressure tested under water. However unlikely (to me) it must be leaking somehow.
Also fitted 6 new spark plugs. Old plugs were clean and wet. New sparks made no difference.
Ordered OE 4-way connector and a domestic sourced garden X connector. Whichever comes first will be fitted.
Also ordered new OE HT cable kit. Will replace the high voltage aftermarket coil/cable setup with OE only.

Somehow I will get it going properly. Really appreciate all your help and support!
 
Ordered OE 4-way connector and a domestic sourced garden X connector. Whichever comes first will be fitted.

Ok good. As unlikely as it seems, it and the 4 way to MAP sensor is where the vacuum strength has fallen down according to your testing at various points with the independent gauge.
Components can be built different for vacuum than positive pressure, and behave differently when damaged too.

While waiting on the 4 way to arrive, I would go back to the start and pretend I just encountered the problem for the very first time, and start from scratch with all the diagnostic testing and verification. Leaving no stone unturned.
It is easy miss something and then never go near it because once thinks they covered it.
You can also have a situation where the faulty part works just for the test, or where there are 2 or more faulty items and they all conspire to make you lose your mind.
 
Following up on @R-III-R Turbo's suggestion:
  • Is it at all possible you have the spark plug cables routed incorrectly (going to wrong plug)?
  • Also, crimp thin wire leads to all three coils (#1 in the head stock is a

Following up on @R-III-R Turbo's suggestion:
  • Is it at all possible you have the spark plug cables routed incorrectly (going to wrong plug)?
  • Also, crimp thin wire leads to all three coils (#1 in the head stock is a b*tch)
I have a custom setup with high voltage coils and carbon HT leads (oe spade connectors are long gone) that is correctly routed. But I will revert to stock setup simply because I cannot eliminate ignition as a problem source.
 
This has been a long thread and perhaps I missed something but if you are testing all the vacuum lines maybe the culprit is the map sensor that is broken so that it loses all the vacuum. A good vacuum pump checker and some surgery pliers works wonders when probs with vacuum.
It may be useful to know that the rocket has a flood clear mode
You just twist the throttle wide open and the ecu cuts gas while cranking when release throttle to about 2/3 it will then start with about 4000 rpm.
 
When you replaced your cam chain, did you replace the gears as well ? It's possible to bolt them onto the cam in the wrong position. The timing would appear correct going by the marks on the gears, but the cams would be off.
I did change the gears, but I can't see how I could get the very good compression readings that I do if the sprockets were off.
 
did you spray starter fluid or propane around the base of the throttle bodies to test the base mounting yes or no?
did you unplug the connector on the map sensor to see if that would help yes or no?
did you take a vacuum pump and hook it to the map sensor and pump it to 18 inches of vacuum to see if that works yes or no?
maybe you just like working on the bike
 
I'm not sure either, just putting it out
It could very well have been the problem. Been off with the head and front engine covers twice to check. Started a thread in another R3 resource specifically addressing cam gear position and got thumbs up. Finally got a precision compression gauge to be sure valve movements were correct. Although, I don't actually know if excellent compression values = correct timing. It just makes sense to me that all valves must be correctly positioned for all 4 to be closed at TDC.
Wouldn't mind getting that theory confirmed through