For some reason, we still haven't solved the basic problem of getting the air out and getting good flow through the loops.
Your system looks like a figure 8 with the tank as the center of the 8. It is the X part of the 8. If you simply valve off one side of that 8, the manifold side, on both sup and ret lines, then add tees next to the valves, you can flush that side of the 8. Flush both pipes, the pump, the manifold and the loops all at once.
Remember, the center of the figure 8 is an X, That is where the tank is. It's the X. The supply line comes from the X and goes to a valve, then a tee (tee 1) then the pump and then the manifold, then the return line comes from the manifold back to another tee (tee 2) then another valve and back to the X (tank). Both tees have hose bibs, or tee 1 has the auto fill instead. The flow goes toward the manifold hot side, or red side. I don't know if your flow meters are on the supply or return (hot or cold) side. Watts manifolds have them on the hot or supply side.
Now, fill the system (manifold side of the X) at tee 1 with your auto fill. Then close both valves and open tee 2 hose bib to purge the air out of the pipes, the manifold, the loops and the pump. Done.
Or, with no auto fill, connect a hose to tee 1 with a bib instead of the fill valve and use city pressure to blast the system out. Auto fill is better.
Now, open the valves, close the bibs on the tees and start the pump. System pressure should be at 10 to 20 PSI to begin. Static cool pressure later should be set a 12. If air gets into the pump again, open tee 2 hose bib while it's running to force the air through the pump. You can close the supply valve with the pump running to help with this process, if needed. With no air, and the loop restrictors open, and the flow in the right direction, you should be seeing about 1 gpm at each flow meter and the pump will be quiet.
Maybe your flow meters are simply stuck and you are getting flow. Could be. With everything running and most of the air out, slowly close valve 1, before the pump, and listen to the pump as you do. Does it's sound change? If so it's probably pumping. If it's pumping you have flow in the loops. It's sound may change with pockets of bubbles going through it during the startup process. Listen for this. A grinding sound that will come and go. That's good. It means it's working. Once it's working it will clear itself completely over time and become silent. It's performance will also increase and you'll see a higher flow rate. A steady grinding sound probably means it's air locked and you should open bib 2, close valve 1, to clear it or help it. Just fiddle with it
and look for sound or visual changes. Give it some time to get things sorted out. Adjust the pressure to make the bubbles smaller if needed. You can even glance at it with a wary eye to let it know your watching. You might have to come up with some new words in the process, but it's only air, water, gravity, pressure, a few valves and a centrifugal pump. What could possibly go wrong?
Put a similar set of valves and tees on the other side of the X to fill and purge the heat exchanger side if needed (I'm not sure you do need them there).
Fill the tank. You can close valve 1, open valve 2 and let the auto fill purge the system by sending all air and water to the tank through the manifold and return line. Then the auto-vent you installed on top of the tank will vent the air. Meanwhile, your thermosyphon lines from the heat exchanger, that slope upwards, should let air trickle up to the tank and get out. In theory, you should be able to just fill it up and turn it on. The heat exchanger pump, if in the right place, may purge during the process and need no further help.
Now get that thing going so we can see how much energy it can transfer.
Install your expansion tank somewhere. It might be best on the top of the tank or on tee 1. You could put a second tee on the line running from your auto-fill to tee 1 and screw it on there. It also can be remote mounted but tied in at that point. That would put it on the suction side of the manifold pump which would tend to make the bubbles smaller in the manifold and make the pump deal with less air.