After trying to make a sump out of a 20 tall and use a Coralife SS 65 in it, I learned the meaning of bubble box... and always running my cheato ball in the section before the pump (cheato slows the flow of water and grabs any of the bubbles that might make it out of the skimmer chamber).
The first step is definitely diagnosing where your bubbles are coming from.
I know for sure that tanks seem to naturally get better a couple of weeks after they've been set up. If you're running a new skimmer (can't remember), that could be the culprit and I'd wait a couple more weeks before getting radical on re-doing any plumbing.
If the bubbles seem to just be coming from the return area, do you have a bubble box?
Do you have something at the bottom of that box that forces the majority of the water flowing in back up to the surface? I honestly threw an icecube bucket underneath of the place that I had my overflows and skimmer feeding into. This takes the majority of the flow back upward where the bubbles break allowing slower moving (hopefully relatively bubble-free) water under the first set of baffles.
Depending on what the output of your skimmer is like, try as hard as you can to get the output of that as far from the pump as you can. I've never seen any kind of skimmer, regardless of cost, that didn't put more microbubbles into a tank than you would want to have get to your pump and into the display.
This may sound stupid, but I know you're probably running a lot of flow in the main tank... are any of your pumps blowing too much on the surface and dragging small amounts of bubbles underwater with the turbulence. I once had a pump that I didn't realize was creating a little vortex at the surface that just pulled a couple of bubbles under the water every once in a while. When you've got a lot of flow in a tank, small microbubbles can stay suspended for quite a long time.
I personally wouldn't rip apart your plumbing unless you think you might have a leak on the suction side of the return pump or a closed loop. If this is what you think you do have, do your very best to isolate the joints that you think might be leaking (the goal being to reduce how much you have to drain your tank or re-plumb) If there is air trapped in your return plumbing, it should work its way out as long as you keep the return running, so if you suspect that, just don't shut it off for feeding for a few days and see if they stop. If air is getting trapped somewhere and is just slowly releasing into the aquarium, try re-routing the return plumbing so that air doesn't have a place to gather (if you have a loop or something in the plumbing).
Anyway... that's all just stuff I've learned to try. Good luck.
