Hi... on my last pond... I had similar vertical loops on my old pond and those ones never seemed to give me headaches while running... Other than when coming out of winter mode, which was when I found placing back checks as far as below the waterline as possible were far more easier to prime, remove 1 clean-out cap, fill with hose & flip the switch and blow everything wide open on charge... During all season it never ever lost prime. Even when down for maintenance, whether it an hour, a day or seven days even, ever trapped air and never saw bubbles or foaming anywhere (or I never noticed anyway)... other than one time when my son, very young at the time, dropped a bottle of blowing-bubble soap in it once...
And I do agree odd ups & downs for flow control but, the raised garden beds sort of dictates it so I'm kind of stuck doing that....
I suppose my biggest "whats" on this one is whether to keep with 3" plumbing end to end or maybe scale it back and drop to 2" end to end (other than out of the BD)... This setup is so small compared to my last one and that was all on 1.5" pipe and that never had issues, but now with 10X the pipe run in length and going 2X the pipe Diameter...? And I'm sort of confused as I see many builds all plumbed in 3 or 4 inch pipe yet when it comes to building the SG they're running 2" and even a few plumbed with 1.5" . So it makes me wonder if I should be using 2" end to end or keep with 3" but if I have to reduce somewhere or anywhere then whats the point?.... And most of the pond examples/builds I look at are much larger than what I have going on here.... I understand the basic needs but in the same token I'm not trying to not to turn it into rocket science either...
I do have one other spot I can try to slip in the pump that is extremely close to the pond & below waterline it might even be possible... I'll update the drawing and see if it's better or fits there...