Finally some updates for this. I was having quite a bit of issues after putting the top end on. I was having all sorts of issues with cylinders missing. While I was looking into all possible problems, and driving it to work. I had at least one of the rockers start to continually loosen. So, although I was hoping to avoid it, I pulled the cam. Multiple lobes were wearing or almost gone! I just happened to have a Comp XE268 laying around, so in it went. Solved some issues, but then I still ended up with plugs becoming very black and sooty, they were dry as well. Didn't trust the 600 that was on it, so I threw on a 750, that seemed to be on better working order. Thought it was good but after about ten miles the car started to miss again. And I mean cutting out popping out the exhaust etc. So it sat on the back burner for a bit.
Next I threw the 750 off the Malibu that I knew 100% there was nothing wrong with. Same problems.
Today, problem solved! Left the hood off and it was fine. It seems with the even more reduced hood clearance from the new intake it must have been acting like a choke. Now this had crossed my mind before but I had ran it with the hood off and was still having problems. In hindsight the last time I had the hood off, it still had the bad cam in it.
More pictures to come.