For sake of input, Jdupree's 222 CCP used the same system with a mushroom....it wouldn't prime consistently. He changed it to a clamshell, end of issue.
I didn't realize JD mounted a mushroom under the hull. The CCPs of that era came with a "scoop" of sorts mounted on the transom that flowed water into the transom mounted live well. No shut off valve, just a piece of pipe running into the well. It was a glorified hole really and I never found it to be much good so I removed mine and sealed up the transom. Live well became a trash bin. 
I could see how one would have difficulty pulling water through that and sending it to a different location. I'm surprised his under hull mushroom didn't work with the diaphragm pump.
He didn't mount a mushroom...it was like that when he bought it. We both figured it was factory, as the example (pic) above. Exactly the same fitting.
Straight pipe on yours...no seacock....weird, especially since it was factory rigged.
John's has a seacock, hard to turn. He has loosened it up, but still hard to turn.
He no longer uses his built-in livewell either. He has a new setup under the leaning post that works great.
Re the mushroom and the clamshell...the mushroom is latent, the clamshell forced. Even with a self-priming pump....as opposed to the forced clamshell raw water pickup, the mushroom intake provides frothier froth the faster you go.
As you say, a true pickup is the way to go.
