PANAVIA OK here goes.
EAsy stuff first, Valve covers hitting the rocker ends. If you like the valve cover you have, you are going to have to mill or grind the end supports to clear the valve covers. If you don't want to do this, one of the guys here sells spacers that bolt between the head and valve cover. Just need a second set of gaskets and it gives about 3/4" of height.
Rockers and pushrods, the camshaft is a little big with over .600" lift. You are going to need a dremel tool to grind the area behind where the adjuster rides. You want about .030" clearance on full lift of the pushrod to the rocker edge. You also need to remember that the motor is a living thing and expands when hot and scrinks when cold. Don't go crazy on this modification. Remove as little material as possible for the clearance. Min. of .080" orifaces in the head for controlling
oil to the rockers. This
oil also cools the valve spring which produce alot of heat too. I doubt that you ar going to be able to center on the rockers on the valve ends with interferance of the intake manifold. The important thing is to have clearance of the pushrod through full movement from the intake. As long as the rocker wheel is in the center of the valve stem this is OK. It may be a little off to the right or left on the valve. Over time this may wear out the guide or valve and need to be repaired or replaced.
For the adjuster on the rockers I would tell you to buy the valve adjuster tool from LSM Nice tool that turns both the adjust and a torque wrench to lock it off and not over tighten the nut. Look under LSM PRODUCTS.
1 Question How did you order the pushrods if you didn't have the camshaft and rockers on the motor? It sound like you could also have the the wrong length. If too long you would have the pushrod hitting the rocker on the inside too. If too short too many threads sticking out of the rocker at the bottom. Some where in this forum is the correct setup for rockers and how you want them to stay centered on the valve stem if you have already not done this. I don't know if the block was machined square on the cylinders. They could have removed from .005-.020" to get a new flat clean surface. This will knock off the corrrect length. Recheck your build, if unsure go back to the beginning and recheck to make sure that everything is square. Intake to heads, heads to block, intake clearance on the block and so on. .020" doesn't sound like alot, but it could cause the pushrods to hit the rocker with out any modifications. Been through this may self with double order of pushrods on my motor. The nut on the adjust pushrod came loose and knocked off the roller rocker from staying in the center of the valve stem. Good luck. I think Tom Lucas sell valve spacers but not sure. Google it. Rick L.