The burn mark between 3 and 4 is only between the two cylinders and doesnt extend beyond that. I don't believe this is going to affect anything other than your compression between the two cylinders.
Since you mentioned all the buildup of crap you had to scrape out. If this was plugged, it is probably enough to cause backpressure in the crankcase, forcing the oil into the intake manifold.
I'm betting that as long as your head isn't warped, you can slap this thing together and be up and running. From the pics, the internals look pretty clean to me.
It was probably a benefit pulling the head and seeing that scorch mark so you could replace that head gasket before it went completely out.
