New 408 stroker runs rough at idle

ok so I killed the spark to each cylinder 1 at a time, and the idle drops noticeably for cylinders 1 and 3. The rest make literally zero difference. I pulled a plug on the number 7 cylinder and it’s black. And so is the number 1 cylinder. The number 7 plug wire has a very hot spark. Anyways, I put a vacuum gauge on it, and I’m pulling 8 inches idling at 850 rpm. The vacuum climbs up to 18 inches at 1500-2000 rpm. I live 5000 ft above sea level. Then I noticed the vacuum plug for the pcv port was slightly loose. I messed with it, took it off and plugged my finger in there, and put it back on, and now it idles a lot better. I then happened to notice the fuel filter which is clear plastic was empty, with just short spurts of fuel coming from the fuel pump side. But the engine stays running. Is this normal?