I know what you mean...took the bike for a run yesterday - she ran beautifully...no issues...then, a couple of times on the freeway the engine missed when I indicated (only once or twice) and just as I was getting home it seemed to be running a bit rough and stopped - started again immediately and i got home. I started it up again and it seemed to run well, with no issues when I turned the indicators on and off - I don't know what is going on...just when I thought I had it fixed...

Sounds familiar , except I thought I had mine fixed about 20 times. What is happening here is there is a bad connection in a main power supply wire, and when you put an extra load ( blinkers, head lights )on this failing joint the voltage downstream of this joint drops to the point where the ecu will no longer function properly.
Follow the power from the batt to the ecu and to the coils , and check every switch and plug on the way. Chech the terminals on the ends of the wires carefully , I have seen the copper strands break between the 2 crimps on the terminals. I would just replace the plugs at both the RH switch block and the ignition switch , trim at least 1 cm off the wires before reterminating.
The coils are earthed via the ecu , so make sure the ecu is well earthed. If you have a multi meter and know how to do a volt drop test this will help heaps

Thank you for your help. I will have a go at tracing the wiring again. What puzzles me is that everything seemed to run really well for quite a long time and then didn't...and now seems OK again. That doesn't make a lot of sense to me in terms of a bad connection - ie I would have thought the bad connection would be bad from the start and not get better and then worse again (and then better again!!) - although I guess vibrations could cause this.... I wondered if there was a heating problem - ie the bike heated up and caused the problem - and when it cooled down it got better..not sure I will have a lot of time in the next few weeks to look at this -some overseas work and the the motogiro will keep me occupied for a while...
Take care

IF the electrics is completely fine, the grounds are good and clean , there are no shorts etc it could be that the coils fail under heat but i doubt that as you say the misfiring is connected to the turn signals. If it were the coils it would start misfiring by itself after some time.

G.

One of the symptoms of a bad connection , especially on something carrying a bit of load , is that it gets hot, and the hotter it gets the worse the connection gets, so it sort of snowballs, which is why it seems ok at the start of the ride.
All the green / black ( power wires ) are connected together in a blob of solder inside the harness so dont waist to much time trying to find the terminal block that aint there ( ho hum )