The pipe is gravity fed. Trapped air, residual mud, and high spots in the pipe are all suspicions.

Yesterday I found a high spot in the pipe caused by a root from a growing tree. I was able to dig to the side and slide the pipe slightly to the side and down into a new "trench" that I had dug. I'm sure it helped but I couldn't observe much difference.

I probably have more high spots since the pipe is only on a shallow gradient. Would a construction level (or laser level?) be the best to evaluate and find high spots?

I don't think I can suck water using the trash pump, as only about 1/4 of the six inch pipe has water at the outlet. But its full and submerged at the inlet.