More exhaust comes out the left (port side of the bike,
clutch side) which I find odd. I'll let you two gurus determine sealant or no sealant

Couldn't I just flush oil through a few times to get the dirt out instead of running it through the engine?
Clutch side is on the right or starboard side (above your rear brake). That right side, at least for my Scorps are straight thru with the Y branching off to the port side..
Pulling the header, pan and doing all that over won't hurt anything, but
IMO, is way overkill... (unless the bike is filthy/your sloppy, etc)..
I can gaurentee, NO shop would do that normally
unless you asked and paid for it..
As I re-call, (Randy correct me if I'm wrong), FI simply changed the oil with your last valve adjustment. This is the FIRST time
any mention was made of removing the pan and header for a simple valve adjustment...
*Another option, is to drain the oil before hand and keep it covered. Do your valve check/adjustment, then pour that oil (which is not contaminated) across the valves / head and let it drain into the pan. It'll flush down any crap, now drain it... Now put in fresh oil / filter.
Personally, I'd clean the upper frame, top of engine, any place dirt can drop, spotless clean. Take care of business...
As for the sealer, it's NOT called for. You'll see Yamaha put a sealer on the gasket already. Can it hurt to add more, only if it oozes into the block.
I've replaced both the rotor cover and cam chain cover on mine (rotor cover 3 times). Sealer is not called for (except where the wires come thru). Same thing, the gaskets have sealer on them already. They are bone dry 20,000 miles later.
Look at your cam chain cover and you'll see you'll be scraping gasket material from the block, cover or both. No sealer
In the scheme of things, it's not a biggon, getting the valves set correctly is...