I thought I would start a different thread for this.
After running for about 15 - 20 minutes the ECU cuts out sometimes both cylinders sometimes one. I thought it might be a bad temperature sensor so today I substituted fixed resistors in place of the sensors.
Heres what I discovered
First of all I loose 1 cylinder. On feeling the transistors I find the two spark FETs are quite warm, not enough to burn but getting up there. The transistor in the center of the board is warmest. I put this down to the distance from the ground plane at the edge of board. I assume this is the one that cut out.
My FETS have the two little heatsinks that Cliff provided along with some heatsink compound.
The injector FETs stay nice and cool.
After sitting for a couple of minutes the bike will start but soon cuts out again.
I have no cover on the ECU at the moment.
It was a very hot day ~40 C.
I have 5.3 nF 1000 V (ncd472m1kvz5) ceramic disc capacitors wrapped around the pins going to the two large tracks.
Could it be these capacitors?
Do I need a better heat sink i.e. a thermal connection to the case?
Hope someone can help.
Roy

Both gates read 0.027 V to ground (Fluke 87), there's zero on the other two terminals (R5 is not energized)
With the bike idling I read ~0.3 on the gates
Yes coils are 0.7 Ohms
I will hang my scope on the gates tomorrow and report back.
No, I made no changes to the coil charge time but I will look at that also.
Thanks
Roy

7ms sounds a bit excessive. It should be around 6ms from the map entry coiicharge0=6000.
This is for starting only.
Once running it will revert to the coilcharge1=2700.
Check this is the case otherwise they will overheat.

I'm surprised the voltage is ramping up so high. That does seem too high. Those FETs don't have a low Rds because they are high voltage FETs. I'd expect about 6V across them.

The 6000 looks like it may be too high. I think everyone might benefit from a reduced value  to say 4000. Or it could be your test scenario because normally the voltage is less than 10V due to cranking.

Ok, I gave the map a 20% increase in injector time 2-5000 revs.
The bike seems much happier now I went for a long ride and it only cut out once after a run at 3/4 throttle. I measured the transistor temperature, only 35C so that's not a problem.
Here's my theory the previous run it was a very hot day, the map was way too lean, it was a hot day, the air sensor was hot, the oil sensor was hot so the bike cut out on lean mixture.
Today was quite a bit cooler and the mixture was richer and the bike ran OK until I ran at wide throttle where the map has not been richened.
Does that make any sense at all?
Can someone explain the effect air and oil temperature have on the map, does hotter sensor make the mixture richer or leaner?
My mixture is still too lean at low revs and low throttle setting misses quite badly but as soon as I soon as I wrap the throttle or the revs are over 3000 it settles down and pulls away.
Needless to say I am much happier 

So much for that theory then, the temperature sensors don't have a lot of effect, I assume the +# is microseconds injector time so for an injector time of say 3050 +5.5 is nothing, or is it %? Never mind, I see it's percent boost.
So going from ambient 20°C to 30°C I loose 10.1 + 3.4 = 13.5% fuel
I am still puzzled over the map table Flags. If I look at some maps it's mainly populated with o0 & o1 (derived from Sport11Stock) wheras other maps have a wider range o0,o1,o2,o3,o4,05 (Derived from code as flashed by Cliff - I think). My understanding of flags is bits set by the program but the character o "oh" isn't binary or hex. What sets these flags? Is this perhaps refering to the O2 targets e.g. o4 calling for O2 target of 0.80. There are 8 O2 targets, which is o0 and which is o8?
Running open loop shouldn't all the targets be o0 or does it just ignore that line in the code?
I think my ECU Controller always shows closed loop even though I have selected None for sensors under MyECU Config.
Bear with me, I'm learning here, I'm sure others are as well 
Leave me alone long enough and I will probably figure it out.
I must ask Cliff for spellcheque 
Roy

Thanks Cliff, I found the good "Maps Explained" topic on the Technical Site. I will study this before I ask any further
Perhaps a button linking to that site would save a lot of questions.
Still making progress, the bike runs better with each change I make.
Update July 15th
I found a major faux-par tonight. When I started out I changed the pressure module setting and it read correctly but I must have accidentally overwritten the file because tonight I noticed the barometer pressure showing 580 mb, obviously this is having a major effect on the map and accounts for my having to en-richen it across the board.
Actually I think it was caused by software problem with the 10 year old laptop I am using, if I open the file in notepad when I save it it changes to a text document that I can't see with the MyECU software. No matter what I tried it always does that.
I will fix the file with a better laptop and start again.
Cheers
Roy

Found it - thanks

http://www.jedit.org/
is worth a look, I also had problems initially with the text editor on my MacBook. Took a while to work out why my modified ecu files were being saved but not running - all sorts of bollocks were being added. Anyway this editor doesn't add any superfluous codes or formats and can be used in Windows or Mac OS environments. AFAIR it's free.