318 poly w/ carter AFB rough running especially idle and off-idle.

Hey my 318 poly is running rough especially idle and hesitant/rough when accelerating. It's not terrible but it just doesn't sound or feel right. I'm think the carb may need to rebuilt and already ordered a kit but I have a few questions.
BTW, as of yesterday it has all new spark plugs, wires, cap rotor, points, condenser, and the timing is set to at exactly 15 before TDC. The car has a mild cam (previous owners words) and a cast iron four barrel poly intake.

- I have a carter AFB 9636 which is the emmission control type. How do I make sure this is hooked up to work on my car best. There are 4 various rubber plugs on fittings and I'm not sure if they should be there or what?

-The accelerator pump seems to work when I push the throttle it squirt's gas. how likely is it that is not working well enough? I took the top of the carb off and the plunger seal is not damaged.

- the carburetor is missing it's fast idle rod, is this my problem or do I not need that neccesarily.

- the idle mixture screws seem to seat funny. One mixture screw feels normal: I screw it in by hand and I can clearly feel when it is lightly seated. But when screwing in the second mixture screw I feel slight resitance before it seats. Also when I take it out fully it to inspect almost seems like there is a spiral shaped seating mark. On the first screw the mark is normal. Is my mixture screw seat possibly damaged and how can that be fixed?