Even when these motors are running perfect there's always something that breaks or needs to be replaced and it always turns out to be the stupidest little thing in the hardest place possible. Well it seems you've ruled out just about everything. While you've got it apart check the coolant passages in the lim and heads, also check to make sure the pipe that screws into the back of the thermostsat housing is free flowing and the return line as well. Other than that I wonder if it could be something stupid like the radiator cap isn't holding the correct pressure or for some reason your fan isn't working or kicking on at the right time. And no the thread locker on lim bolts shouldn't be a problem, unless your going to take them off again it may be difficult to remove them. Taking this thing apart and putting it back together right is not a simple task. So kudos to you on that. Keep us updated on what happens.
