Idling issues

Plug checks are usless for adjusting the mixture screws. Get the engine running and warmed up then adjust the idle mixture screws for best idle. If you have the Dyna S ignition you will still have the the mechanical advance adjuster and you still need to check that for smooth operation.
It sounds like you still have a vacume leak. Are the replacement manifold new or used? If used manifolds, then take them back off and apply a thing layer of Yamabond #4 or equivalent to the mating surface re-install and wait 24 hours before starting bike. I have had new manifold leak and the Yamabond sealed them up. While you are waiting for the manifolds to dry clean the carbs again making sure all the small passegways in the carb bodies are clean and clear.
Also make sure throttle cables are free and not binding.

I put new intakes on it but used the old clamps and they are kinda messed up. I'm gonna get new clamps and try the Yamabond too.

Question about the fuel mixture screws. We are talking about the brass screw right in front of the filter correct?

While the bike is running I should turn each screw in one direction 1/4 of a turn at a time until optimum idle is obtained correct?

Yes those are the Air Screws for the Idle circuit. These when turned out will add air to the idle circuit, leaning out the mixture. I'd start at 1 turn out from lightly seated/ closed. With the pods it will be a bit leaner already than with the airbox.
Have you Just added those Pods? If so you'll be raising the needle a clip, and increasing the main jet a couple of sizes before it will start to run right. More tuning after that also probably.

The bike had velocity stacks on it when I got it and it didn't run very well so I put the pods on it. With pods, the needles should be in the middle position?
I have 120 mains and 20 pilots in it now.

120 mains, #20 pilots and the clip in the middle spot should get you in the ball park on jetting, do you have a 4 into 1 pipe or the stock exhaust?

Kerker 4 into 1 exhaust. I'll check the clip position.