Cool set up! I have a similar though much smaller one (5 gal), so here are some thoughts...
-insulate the MLT and put a lid on it
-put the temp probe on the outflow from the coil, so basically just before the wort goes back into the MLT
-increasing the flow rate probably would help, but I think it's more important to get your strike temp right so that the system doesn't have to fix wide variances in temp.
-higher flow rate will be more important if you want to do step mashes
Where are you seeing the air bubbles?
As far as process, I use my boil kettle for heating the strike water and only heat my hot liquor to the mash temp. I have my probe on the overall liquor temp during heating, then switch it over to the outflow right before it goes into the MLT.
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