Picked the bike up yesterday (Monday). Bike working ok, took it for a 90km spin when I picked it up.
Tuesday (today)  another 150km bike lost power about 4 to 5 times for about 1 to 2 seconds in a two minute period then continue 50km without fault.
Will not be taking it back to the shop that did the work, they did spend time rechecking plugs and wires and soldered some wires at plugs to improve connectivity.

Not sure what the next step is apart from rechecking wires myself.

I'd check the TPS if it hasn't been done yet

I will thanks.

The symptoms you described match. In case of failure the TPS usually "underestimates" the fuel flow required, which then leads to fuel starvation ...

So in my opinion the TPS is a good candidate for replacement. If this hasn't been checked already, we're talking gross negligence (from the shop). They should have thought of it.

Thanks Tartofraiz,

 I’m in the process of having the bike tested properly with good technology. Will hopefully have it sorted in the next few weeks.

 I agree the tps should have been an obvious call for the bike shop...
 BUT...the anciliaries are all reported to have been at fault too...which does indicate that there is a systemic issue that is frying everything..?
 Yamaha didnt suggest a TPS when they were consulted..?
 This smacks of ineptitude..Do like a Mastiff and chomp down hard, and dont let go til you get satisfaction !!

 

If you had a power commander then the exup and/or the air intake sensors have possibly been disconnected so check them. Power commanders are not suited to the MT unless you’re stage 2 or above in my view and even then very few people have got massive improvements with them.

 Yes and no...
 
  The lean fueling seen on some of these bikes (RP18?) is a good reason ..
 That, and the fact you cannot simply or easily "over write" the ECUs...