@SpookDog Do you still have plain bolts and copper washers in your carb warmer hose connections? If so this could be the culprit. The official Yamaha procedure for bleeding the cooling system is to remove the carb warmer hose where it joins the thermostat housing (i.e above the actual thermostat), then fill the rad whilst watching for coolant to come out of the tube with no bubbles, then refit the tube and fill the radiator to the brim with the bike vertical. If your carb warmer circuit isn't operating you'll have a small air pocket below the thermostat until it opens.
I'm not a huge fan of the carb warmer circuit as IMO it's not really cold enough to warrant it in the UK and it makes getting the carb off a right PITA if you like experimenting with jetting, float heights etc. But it has another useful function which is to make the cooling system self-bleeding by allowing it to bypass the thermostat during refilling (this is why bikes like the 350LC without a carb warmer circuit have bleed bolts on the sides of the cylinders). So the best compromise I found was to just run a single hose directly from one banjo to the other, retaining the self-bleeding and not having to disturb the cooling system if/when taking the carb off.
I've never primed the expansion tank circuit and I'm not sure it would be necessary because as the coolant expands in use and travels down the tube, it would probably expel any air present anyway. But I guess you could by filling the tank, then putting a long tube over the filler hole to avoid ingesting any antifreeze and blowing through it until coolant comes back out the tube and fills the rad to the brim, then sticking the rad cap on quick and topping up the expansion tank. And definitely fill the rad slowly as @OllieDTR said.
TBH I'd try refitting the carb warmer banjos first and see if you're still getting an air gap in the rad. When I sold Greta the other day Liam asked to see the coolant level as I mentioned I'd replaced the head gasket when I bought the bike, so we took off the rad cap to look and the coolant was right to the brim after being ridden a few thousand miles (including getting quite hot off-road a few times) and being in my living room for over two years.
