318 running rough and losing vacuum when in gear.

I would Start with a compression test. Seems like you have looked at the basic problem areas. At first I thought the coil but I reread your thread. Next would take off a valve cover and look to see if any valve train is bent or broken.
Yeah I did all that when I swapped intakes yesterday. all plugs were nice and golden just like mcdonald's fries. so don't think compression is the issue put will check it. thanks