Make sure that PCIII is grounded securely to the frame or battery and that the connection to the TPS wire is soldered. I had issues with the bike stalling or not starting due to those two connections to the PCIII failing.
You can also check for any MIL codes. Check battery terminal connections and the ground connection to the frame under the tank.
Don't know what the shop did, but I don't think you got your money's worth.
2012 Yamaha Super Tenere
2001 Honda Blackbird
2007 Honda 919
49/50 visited on two wheels. 1 more to go!