1) I agree that the service department almost certainly screwed up something. The bike was working correctly when it was dropped off but not so much when it was picked up.
2) The single most likely screwup, based upon what they said they did, is messed up valve timing by a tooth.
3) Just because a dozen people (including me) have said that it is a skipped tooth doesn't make it so!
4) Wailing and gnashing of teeth will do nothing but put the dealership on the defensive and won't help you get your bike back any sooner! Same with threats and unsolicited advice from an Internet forum (whether it is right or not).
Perhaps we can confine it to stuff that might have been touched/adjusted/moved or otherwise fucked with as a function of doing a valve check.
Vacuum leak - loose or damaged vacuum line, loose or damaged TBS rubber cap
TBS - thoroughly messed up somewhere along the line
Broken or damaged COP - can happen when removing wires/plugs. OOPS, I just saw that it was a 2012 so no COP but a reasonable chance that a plug wire or boot was damaged.
Screwed up cylinder identification sensor - broken or re-installed wrong
Damaged or just plain bad spark plug
Damaged or bad throttle position sensor - there have been a couple (But not on Gen II, AFAIK)
Damaged or pinched fuel line - I admit this would be worse at higher RPM than at idle
Gummed up air pressure sensor. I had this happen with my '07 but I'm pretty sure it would throw a code.
https://www.fjrforum.com/forum//index.php/topic/170314-fault-code-14-gen-ii-solved/
Hopefully, the cam retainer caps were re-installed and re-torqued correctly. If mistaken, it would show up in a post-adjustment clearance confirmation, if they did one.
If they did not do a post-adjustment check, there is a distinct possibility that they used the wrong shims and put the clearance WAAAY off. Can't imagine how bad it would have to be to cause it to run this poorly.
There is also a (much less likely) chance that something has happened that was unrelated to the service that was performed. (i.e. fuel injector etc.) Coincidental failure is unlikely, but still possible.
Probably lots of stuff that I haven't considered. Just trying to make the point that the most likely problem isn't necessarily the only possible problem.
Hoping that the service guys can get correctly diagnose and get you going. Perhaps Yamaha Corporate can/will help. Good luck!