make the overflow quieter by putting a piece of airline tubing down the drain hole...you'll have to move it up and down until you find the sweet spot, then tape/glue/fasten it in place so it doesn't fall down the drain.
good deal with the partitions in the sump. i think that will help with the micro bubbles. you can also correct the micro bubble issue by installing an ATO (auto top off) to keep the water level towards the top of those partitions.
10" for the skimmer is fine, but i definitely wouldn't waste the rest of that tank. take a couple more inches off if it makes you feel better, but i think that tank is 17" tall, right? you are going to waste almost half of it for a buffer zone, when all you have to do is plan the plumbing correctly to minimize the back siphon.
you could leave the 1" pvc
, and just put a ball valve at the exhaust port of the pump. this would allow you to dial it to whatever you need, exactly.
there is bacteria on all surface area in that tank. even on the granules of sand. a 3" sand bed is a bad idea, because it's not considered a "deep sand bed" because they need to be 4"+, so you are just wasting your money on extra sand. 1"-2" is plenty. it won't hurt the rock.
i have no idea about the moisture on the back pane...wipe it off and see if it comes back. this must be addressed asap!
the bio load on that rock and sand in the bowfront sustains those creatures in there now. if you transfer them over all at once it should be fine. you can also cycle the 50 then put them in. whichever you choose.
btw, are you going to add any more rock to the 50/ if so, that rock will need to be cycled.
btw, if i can explain anything here better on the phone, it would be no problem.