I think I got all of them, you can update to 0.5.12 and it should solve the perf, the save size, and maybe just maybe the biters are going to chew through you pipe wall. One of the main cause of lag was that you had thousands of biters trying to pathfinder to you base basically like every tick, and they should've attacked the nearest building if they can't pathfind to a protestable building, but that was stuck. So now sorry but your pipe wall is inefficient.
I must say you have soooooo many protesters (those had perf issues as well) and I am wondering if there are really that many that you can't keep up, is it too hard ?