I have a 1997 Mercury Villager/ Nissan Quest. I had a water leak and removed the upper intake manifold (plenum) and replaced the gasket. I put everything together and it will turn over but will not start. I got it to start and run for about 2 minutes and it was running really rough and idling real low and check engine light came on. I am trying to get my hands on a OBD2 scanner, but what should I check in the the mean time. It looks like all of the hoses and electrical connections are good, but not sure.

Sounds like you have a vacuum leak , recheck all lines .

Are you sure that you cnnected the MAF sensor back up.