"And there is a hard plastic vacuum tubing that has to be plugged into a double connector deep in the valley. It pops out if you raise the plenum too high."
I know which line you are talking about. I think it's actually PCV line.
When it pops out of the rubber boot best way I found is to crazy glue back into rubber boot deep in the valley first. Then after putting the plenum down, lift up the front, slide rubber hose back on to connection attached to the plenum and finally use a needle nosed plier to slip the metal clamp over the connection.
Another tip is to have replacement weather pack connectors on hand just in case you crack them while unplugging. Those things go real brittle sandwiched between the plenum and valley.
