I converted my stock hot air-style choke into a manual choke, so I've ran into this. The vacuum line coming of the choke goes into the intake manifold. This participates into opening the choke. Thats good that its plugged off. That will not make your idle rough. I would guess that your choke is near closed, thats my guess on the rough idle. It should be open only a 1/4 inch. Then as choke and truck warms up, it should be fully open or close to fully open. I'm thinkin your choke might need adjusted. Thats just my input, lol, MARK