Need help with molding thick acrylic LED lens,

Getting a high percentage of whitish swirls and some "blue puffs" light blue spotting on a few. 3 stage inj spd, very slow to eliminate flow lines.

I think they're from the same root cause: you're too cold on the barrel temps. Cold pellets or gels happen most all the time, but when it's not clear or perhaps white you never see them in the part. I'd raise them slightly little by little and watch the recovery/screw charge pressure. You want to stay around 700-1000 psi on the screw motor. I even bet your starting psi is lower until you begin to run at cycle time. Not uncommon to discover this until you've been running for a few hours. Again, little by little to let the heats stabilize in the process.
Rick.

Contam? What do you use to clean the screw?

If you have ever ran anything in a press other than clear or white you pull the unit down and clean all the parts before reassembling the unit. Do not use sandpaper but brass brushes and copper gauze. Sandpaper can create scratches that end up holding small bits of resin that end up burning or carbonizing.
Rick.

The machines that are running these parts have only been used for acrylic. One is about a little over a year old, the other about 3-4..Other lenses with not as much "body" have not had these issues,but have a different sprue/runner design.Would the feed throat temp have anything to do with it, or sprue/ runner design?Seems to be good around 125-130 but still around 75-80% accepted.

Feed throat temp should have little effect if right and some if wrong or if leaking. If too cold you'll end up burning up the heater band closest to that area as the controller will call for heat so often the heater burns up.
Now sprue, runner, and nozzle should work together to maximize your melt conveyance into the cavity. Do you see the defects in the sprue or runner? If so it could be they are contributing to the issue but I still believe all of this is coming from the injection unit. What are the measurements between this molds parts and the others that run good? It could be due to the residence time and volume of plastic required you need to adjust the barrel heat settings and back pressure and screw rpm's. I still think it's gels or semi-solid pellets from injection unit.
Best mold I ever ran for PC plus UV/FR lenses has S shaped runner with tab gate coming off the side. There was a good cold slug well under the sprue and at the ends of the runner. Ran like 1% scrap and we just turned heats down on weekends and it started so easy every Sunday night.
Rick.

I once had a clear part with a thick section where I’d get swarms of near-microscopic shrink voids producing a sort of foam that appeared as a small, opaque (white) defect. More of a tiny potato-shape than a swirl, though. If that is your problem, then you would increase mold temp, increase pack pressure, and increase cooling time. Ideally open up the gate as well.