doesnt take much of a valve leak to make noise in the intake or exhaust. If it isnt a valve issue causing the low compression, it is very easy to get the pan off, and pull that rod and piston.
I would stay with the aftermarket exhaust manifold, the 6.5 manifold doesnt fit this body style very well. Just make sure you put some bosch 80034 plugs in it before you put that downpipe back in.