I've been dealing with a rough idle and low vacuum. Sometimes its not so much noticable but mostly there and annoying. I noticed when car is fully warmed up choke is completely open. (Stock thermostat) I have a 64 and down carter bbs. When its running and hot. I can close the choke flap quite a bit by hand and hear and watch rpm and vacuum rise. How would I go about addressing this?

I'm not sure how the choke is set up on that year, but it would basically just be a matter of extending the choke linkage so that the flap sits closed further when the engine is cold. Pretty easy fix.

EDIT: I think I misinterpreted.
The choke should be fully open when warmed up. If closing it when the vehicle is at operating temp is giving you better performance then the vehicle needs more fuel in its air/fuel mixture.
Try adjusting the mixture screw some to make it run richer. You'll have to adjust idle as well after of course.

Mixture is not the problem idle is set at 775 and mixture is were vacuum gauge is at highest point.

But if you're getting better vacuum and idle when you close the choke when its warmed up, then you're either getting too much air (vacuum leak?) or not enough fuel.