From what you described on the glow plugs your system seems to be working the way it should, check your wts light bulb yours wouldn't be the first one to have burned out or have a bad contact where the bulb holder meets the circuit board connections.

 

86 the wait to start light needs to be rewired since you are using the new style controller.

With the port in the passenger side rocker cover it sounds as if there may have been a turbo on it at one time.

Your options will be to block it off, or swap the rocker cover off the 6.9.
Do make sure that you have a CDR on the rear of the intake throat.
Looks like a tuna can bolted on with two bolts.