Fuel or Electrical?

G'day Figs, sorry, members on this forum all have the Capo1200 and probably don't know what an ETV1000 Capo looks like.......I can only think your fuel problem might be a blockage in a fuel line (I had an FZR1000 Yamaha that had a mystery fuel starvation problem that turned out to be some crud in the fuel line causing intermittent stops).

An earlier bike (FJ1100 Yamaha) had a vacuum blockage in the fuel filler cap caused by a careless mechanic during a rust kill and seal treatment for famous early Yamaha rusting tanks.......so a blocked fuel cap air vent can cause a vacuum in the tank which can cause the motor to stop.

I'd try going back over your service work and just checking everything is connected etc (for peace of mind) and also check for any inline fuel filter gauze's (and pump fuel through the hose to see what comes out). Also, might be an idea to tip the contents of your fuel tank into a bucket and see if it has a build up of condensation/water/bad fuel......

Maybe someone on this very quiet 2013 model Capo 1200 forum has had an ETV1000 and maybe knows what it might be if it isn't a blockage or water in the bottom of the fuel tank etc etc

Best wishes for getting your bike running perfectly again!

Ps just wondered if the ETV was a carby or fuel injection model.....if it has carbies, they might need to have the float bowls drained or the whole carb pulled off and thoroughly cleaned......(a big job.....) - look for the simple fix first......