Garv,
Can't answer everything but may help on a couple issues.
For the chlorinator I have no idea what flow it needs but is there a way you can jury rig a couple lines to your returns and measure the flow by dumping into a bucket or 'calibrated' trash can and timing the dump? If you could break the line that may be easier but then you don't account for the added flow resistance to the returns. Then compute gallons per minute. That would help someone answer the question about low flow to the cell.
Not sure where the bubbles in the pump basket are coming from, may be just trapped, but on low speed you probably don't have enough flow to purge the basket so don't worry about the large bubble. In that place it should not cause any additional noise and won't hurt anything. I assume it's just a bubble right at the top.
On the bearing noise, could be. It would cavitate at high speed. One thing to try is to wait until it does it, shut off the pump, open the pump basket lid to let the water drain out, then turn the pump back on and see if it makes the noise when dry. Doesn't hurt anything to run like that for a couple minutes. If it's a clearance that's changing when warm it will probably do it dry too unless the stresses on the components change because of pumping water, but I doubt it.
Best I can do for now. I'll check in later.
Al
Edit: Do you have a bypass mode for the filter? Don't know how DE filters are set up. When bypassed that should up the flow rate some to see if that changes anything.
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