The overheating itself could cause the misfiring (flashing CEL). When the overheating gets fixed, the misfiring may cease along with the overheating.
I remember Igidy only had a misfire when his engine got hot,.... his issue ended up being coils.
I think you've got compression gases leaking past the head gasket and into the cooling system. The compression pressure is around 170 PSI and can easily displace the coolant that's at a pressure of only about 16 PSI. After the coolant is forced out, the engine overheats quickly.
Is it possible to re torque your head bolts ??? (I'm asking because I don't know,... retightening head bolts may not be a smart thing to do ??,... you may have to do an entire head gasket job or replace all your head bolts.)
I think that leak down test should be your next step,... it may very well pinpoint your problem.