Common issues with them are the coil packs and the connections to them and the grounds on the bike.
Sounds like an electrical issue.
If you want to take it to someone. Imperial is really good. They have done good by me many times on my rocket and my ninja. I needed some scrap stainless and they hooked me up free from a bone pile. If I ever needed a mechanic ( I do not) I would go to them. That or steels. Steels is just pain old school pros with no bs.
I don't have much experience with mechanics as I do or all or learn how to do it... Usually the hard way.
I would make sure the coils and plugs are in working order. Not sure why it was flashed or needs a reflash but that's simple enough. Put new gas in it and if it's not running right check the plugs. Past this it could be a voltage issue from the PCM but that's not so common. Pull the nozzles and give them a quick cleaning.
If you need to clean them have them sent out. I know a guy local who is perfect. He has done rocket nozzles too.
It could be the tps and that's easy to test with the tuning software.