Camal

Something like below.  I've only done 3 as an example but it should be clear enough if you look at these.

You would need 6 aux outputs to do that, do you have 6 spare?

Pre Crank prime is a time based squirt that happens at power up.  All the other enrichments are percentage adder based on the numbers in the main fuel table.
You can log them all to see how much of each is working and how they transition from one phase to the next.  There is a page in the help file that shows the order they work.  I can't give a link today as working from a phone, but if you click on one of the cold start settings and press F1 you will find it.  

Can you try with the dwell set back to ms mode and put a flat 3ms all over.  I think the "cut" might be the dwell getting too short and the MSD doesnt like it.

Sorry had some surgery this morning so my head is still a bit hazy from the sedation, but have you checked the base timing now with the engine running?  Have you tried adjusting the master fuel up and down while running to see if it runs any cleaner when you move in one direction?  You have 0deg in your ignition table so not many engines will be happy at that, try 10 or 15 at idle, ramping to 30 by about 3000 as a starting point. 

An engine needs fuel, spark and compression to run.  You said when it wont run the timing light still flashes, so that mostly eliminates spark as the problem.  We can assume it has compression and is mechanically sound as you say it runs sometimes so we can cross that one off the list for now.  So, the most obvious factor left is fuel.  We can see in the log the ecu is commanding the injectors to fire, but this doesnt always mean there is fuel getting in to the combustion chamber.  The commanded PW is very short in your log which is why I asked you to increase the master, not sure if you done that.  I dont know what the injector size or the fuel pressure is in these bikes so I cant even guess how much PW it needs.  But, there could also be any number of other fuel related problems that wont show in the log - for instance there may be no fuel pressure, or low voltage at the injectors, etc...  The reason I asked you to do a test with starter fluid is it will quickly prove if it is a fuel problem or not and that gives you a direction to head based on the result of that test.  The plugs being wet does not mean there is enough fuel for combustion - it just means there is no combustion.   
 

You dont have barely any fuel going in still.  You master fuel is still only set to 2. Most likely it will need to be somewhere around 10-20.  Also your fuel table just has a flat 7 in it.  Typical fuel table numbers would be more like 30-100.  Import the fuel table I have attached below. will be a closer starting point.
And, as I have said earlier in your other post you need to increase the dwell, the MSD's dont work reliably with 1.0ms at low speeds.  2.0 would be the bare minimum I would use. 
The trigger errors are most likely due to the ecu having trouble detecting the missing tooth at uneven cranking speeds.  It will probably improve as the tune gets better.
Can you try changing the engine type to 2 stroke.  Leave ignition as direct and fuel as sequential.  This in theory will give you the same as 4 stroke with wasted spark(which seems to be a problem), so it will spark every TDC and give more reliable start up.  You will get twice as much fuel so master will need to be half of whatever it needs in 4 stroke mode (probably something like 5-10ms is my guess).
Fuel Table 1.lte

Can you attach your most recent tune.  And a log of it cranking again.