First of all do you have an AQ series or SX series, there is a difference in the AQ uses a metal water hose fitting that can rot out and not seal, but the SX series used a plastic fitting in the pivot housing that can crack and leak water (inherited from the OMC Cobra design).
Make sure your muffs fit well, some do not and leak so much air in that the pump has trouble priming. Remember on any engine that has an engine mounted impeller the water being fed by the muffs must travel UP about 18" through the transom mount and then approx 3.5' forward to the impeller housing. The impeller cannot suck water, with air in that line. It can only move water that is present in the impeller housing. This is why while Volvo brags about their engine mounted impeller, when it comes to running on the water hose an Alpha or OMC Cobra will prime more easily due to the pump being in the outdrive. So for a Volvo, or Bravo you need to use good fitting muffs and have good water pressure.
When the boat's in the water, it's totally different because hydrostatic pressure fills that whole hose with water because its below the static water line.
So you can see why you will never get it to prime in a trough. That works only on outboards, where the lower unit can be submerged enough.