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Another 'simple' thought. Did you put a good brand new battery after all this cranking and previously going flat with the fan on? And is it fully charged?
Perhaps it's not keeping the Voltage. Exactly this had happened to me on other bike when just once the battery went dead (left the parking light on by mistake). Left it on trickle and the bike ran like new, but that was misleading. Somehow it wasn't keeping the charge anymore like it should. I replaced with it with a new one and never had a problem since.

I am with you Kawboy on it. It has to be something simple. Otherwise it looks like a bike in a good condition.
As an anecdote, pertaining to the 'simple' things that might complicate big, many years ago I bought a brand new computer floppy disc drive. It seemed to be working, but the computer couldn't read from it. Back at the shop they were sure that the floppy drive is good, it has to do with drivers or something else with my computer. They said they never had a bad floppy drive, because these things are bullet proof. Finally, after a lengthy back and forth, they exchanged it for another one. Guess what - it worked flawlessly! Sometimes the most unexpected small detail can make a whole lot of difference.

We have started with fresh charged car battery. No change, though starter runs faster.
Kill switch has been checked (bike won´t even crank when switch is off).
Spark wires are kind of mystery as we were told the firing order is 1-5-3-6-2-4. As it is a waste spark system should sparks run 1-2-3 on the left side and 6-5-4 on the right side?
This is propably messed up as we had some issues finding the timing mark when we had the stroboscope sensor attached to cylinder number ones spark wire. If I remember correctly, we had to flip sparks wires between two coils, located side by side under the top frame tubing.
We have timing, we have fuel, we have spark. Clearly it should do SOMETHING, at least run with terrible misfire, but it does not even start.

Every Inline 6 ever made: 1-5-3-6-2-4
Wasted spark pairs: 1:6, 2:5, 3:4
commons.wikimedia.org/wiki/File:Inline_6...rder_1-5-3-6-2-4.gif

Tuomas wrote: We have started with fresh charged car battery. No change, though starter runs faster.
Kill switch has been checked (bike won´t even crank when switch is off).
Spark wires are kind of mystery as we were told the firing order is 1-5-3-6-2-4. As it is a waste spark system should sparks run 1-2-3 on the left side and 6-5-4 on the right side?
This is probably messed up as we had some issues finding the timing mark when we had the stroboscope sensor attached to cylinder number ones spark wire. If I remember correctly, we had to flip sparks wires between two coils, located side by side under the top frame tubing.
We have timing, we have fuel, we have spark. Clearly it should do SOMETHING, at least run with terrible misfire, but it does not even start.

You are right 1,5,3,6,2,4 is the right firing order. When you're looking at the left 3 plugs that would be 1,3,2 1,3,2 . The eyes and the brain want to see something easy to follow and if you look at 1,3,2,1,3,2 pattern, you can see that 3,2,1 pattern I was trying to tell you. The brain can easily follow the 3,2,1 pattern more so than the 1,3,2 pattern but the end result is the same thing.


Same with the right side 3 plugs. They would fire 5,6, 4,5,6 4. When you look at this pattern you can see the 4,5,6 in the middle of the pattern and again the brain wants to follow an easy pattern.

It's just easier for the eyes to follow a simple left to right or right to left pattern when trying to confirm a pattern when following something moving at 600 times a minute.

Sorry if I confused you. I just thought I might try to give you a simple test that I use as a check. Maybe I shouldn't have mentioned it.

Quick edit note here. Looking at your question "Spark wires are kind of mystery as we were told the firing order is 1-5-3-6-2-4. As it is a waste spark system should sparks run 1-2-3 on the left side and 6-5-4 on the right side? " No, No, No. If in fact that's what you have, you need to change 2 with 3 and change 4 with 5. They are out of order.


In 50 years of wrenching on everything from minibikes to my Porsche 928, I have yet to get to a point where I couldn't get an engine to run. It's a simple process. Suck, squeeze, bang, blow. If it's taking in air/fuel, then compression sparking/ igniting and power/ exhausting, it's running. After that we get down to running good by tweaking the air/fuel mixture, timing (ignition/cam valve timing)

After a short break back to Kawa mysteries. This time we disassembled all six injectors and tested the whole pressure rail with injectors intact for any leaks. There was none.
Flipped spark plug wires from coils, did not make any difference.
They are now connected this way:
1+6 wires go to right side coil
2+5 wires go to left side coil
3+4 wires go to upper coil
Is this correct?
Sparks looks very strong, it feels really amazing that this bike does not want to run.
Fuel pump runs (it primes the rail pressure?) few seconds everytime key is turned on. It runs when cranked.
We don't have pressure gauge for fuel.

This is such a head scratcher.
Under normal circumstances according to the manual, you've got the coils mixed up

.

this is copied out of the manual.

Now with a grain of salt. It is possible that the primary wires to the coils are not in the right place but for now lets just try putting the plug wires on the right coils and feed the right spark plugs and see what happens.