The problem sounds like it could be the filter. A 3 PSI rise may not sound like a lot but it is about 7' of extra head. This can reduce the flow rate quite a bit on high and low speeds. So I would focus on fixing that first.

You might gain a little with larger pipe above ground but your underground pipes are not that bad because you have 3 separate suction pipes that act as a single 2.5" pipe and the two returns act as a single 2" pipe so the plumbing is not that bad. If the long runs to the heat pump are 1.5", that will reduce flow rate quite a bit. Have you considered a heater bypass or do you use it all the time?

Also, what kind of check valve are you using? Some models have very high head loss at lower flow rates. If you don't know take a picture and post.