TOPIC:

New used part arrived finally and naturally owner of the bike butchered the old sensor before i had a chance to measure it!
Anyway there is no significant difference between these parts, bike runs really bad with both throttle sensors. After all checking and tweeking we are back in square one, it runs but it runs as bad as it run when this whole drama started.
It looks and sounds like running really rich and feels like timing is way off. There is some black and grey smoke. However we double checked timing dots and marks many times.
I'm running out of ideas and owner is thinking of buying FJR...
It is a hard one to fix as we don't find the main reason.

I feel your pain tuomas. Wished I could be over there to work through this one with you.I've seen some pretty weird things in my time.
When problems like this happen you have to assume nothing is right and go right back to confirming EVERYTHING. As an example, Vw diesels are known to shear the woodruff key between the crankshaft and the camshaft drive sprocket and usually valves are bent. The woodruff key should never shear but it happens all the time. The rotor on the ZN crankshaft is mounted identical to the VW's camshaft drive sprocket. A tapered shaft, a woodruff key and a tapered bore on the rotor.

I'm going to suggest that you start by pulling the spark plug on #6 and set a screwdriver in the spark plug hole and rotate the crankshaft with a wrench and get the piston on #6 up at top dead center (feel the top of the piston with the screwdriver). Then confirm that the timing mark on the rotor is indicating top dead center. If by chance the woodruff key between the crankshaft and the alternator rotor is sheared, the rotor will not indicate "T" for timing and the rotor will be firing the pulser coils at the wrong time. The camshaft timing will be off. Basically, everything will be off.
As I've been saying all along something is really off and having my previous experience with the VW's, I'm thinking this could also be a possibility.

TDC point (cyl 1+6) matches with the "T"-mark on the rotor.

I've not read the whole of the thread but you mention that it appears to be running rich. There is a check valve screwed into the underside of the fuel tank that the fuel return line is attached to. It can become seized & causes over pressurisation of the fuel rail, hence rich running.

Phil wrote: I've not read the whole of the thread but you mention that it appears to be running rich. There is a check valve screwed into the underside of the fuel tank that the fuel return line is attached to. It can become seized & causes over pressurization of the fuel rail, hence rich running.

EXCELLENT POINT PHIL It could very well be just that simple. Tuomas did measure the rail pressure and reported 3 Kg/cm² which is about 42 psi. A little high but depending on the gauge used, it might be ok or maybe not. A change of 3-5 psi could be enough to cause havoc but it should still run don't you think?
If it was off 8-10 psi I see trouble especially when this is a closed loop system and the computer does not monitor the O² and adjust the fuel map accordingly.

Yes we measured the rail pressure and it was around three kilos. Pressure dropped as soon as fuel pump stopped. We also tried to start the bike with vice grips blocking the return fuel line without any difference. This means we tried to force fuel to manifold with all the pressure we got but it did not help. This really strange, as there is fuel, air and spark. Why doesn't it burn the mixture?
As I have worked with cars, there is always hall (or other proximity) sensor for crank shaft(located near flywheel or so) which gives EFI info of engine rpm. Broken sensors give symptoms like starting problems or erratic running and everything between.
So how does kawa 1300 EFI get the info of engine status (running/not running) and rpm? Is it just those three magnetic sensor around the crank rotor?

I once had chevy 6.2d with similar symptoms like this motorcycle, turned out the cam shaft was broken in half, so only half of pistons had normal movement.