Need some opinions on where to go from here...

Is it dual exhaust with no cross over H or X. I had a car here that the one side muffler was clogged partially and the engine was running bad through the cross over in the intake. Fought that until we did a head job and fired it up open headers. Ran great until we bolted the pipes up.

But I honestly thing you have a issue with the cap. 3 and 4 are neighbors only in the cap. Unless you tore up two lifters side by side exhaust on one and intake on the other.