The vacuum line only handles shifting of the transmission. If it was off, the transmission was shifting into 3rd at about 12 mph which would for sure make the truck feel sluggish with the 3.08 axle gears. Or, it wasn't shifting at all which you would probably notice.
The air bubble bring us back to the fuel filter. What filter do you have? If you have air bubbles, air is getting into the fuel supply before the IP somehow. Normally, this is at the filter base on the stock filters. If they are all the time, then it is before the lift pump because everything after the lift pump is under pressure. If it is just a bit after start up, or it starts runs for a few seconds and dies. Then has a hard time starting again the first start of the day. Look at your filter and base.