pulsing filter pump: how to diagnose?

INYO pools is a pretty dependable resource for pool hardware and they are in Orlando. One of the VERY few vendors we endorse (casually.....nothing formal), they seem to have their act together. They will price some options for you that make sense and could even let you pick up if need be. My bet is UPS is next day from Orland to Tampa, anyway.
 
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After going as far with the disassembly as I could without breaking anything, I ordered a new motor and a seal kit. Since that is going to take a week to arrive, I reassembled and reinstalled the pump.

I cleaned all the parts, including the shaft seal, and lubricated the gasket and o-ring, and upon reassembly and reinstallation, the pump was *much* quieter.
 
Century ECM16SQU would work with the relay in the Jandy. Though not made anymore, they are still available online, give more control, and are a very good motor.
i ordered this motor (ecm16squ) and attempted to install it twice, but i cannot get it to prime for whatever reason. i ordered and installed the recommended seal rebuild kit.

the motor seems to run fine, the impeller is properly installed, the impeller spins and speed adjusts up and down with the integrated controller, but it doesn't prime. my current guess is that i didn't fully seat the seal plate side of the shaft seal and it's pulling in air from there. i've double checked the impeller is properly installed and everything else seems to work except for the priming. the skimmer baskets and drains are not blocked and i feel zero suction at the skimmers.

i will check the seal plate side of the shaft seal, but i appreciate any input on other possible causes.
 
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