Ok. Let's see.....you got the right idea. Not sure if you said it or not, but if have the actual meter, you can test one thing at a time. But if you don't. That's ok. If you don't mind an ugly box....With the box you posted above, I would first try and cut those holes nicer and sand the inside and outside of the circle. Basically make it as rounded over as possible. Then work on the port. Sand, sand, sand. Round over the port on the inside, no sharp edges. Then outside of the port. Round the outside edges, making a kind of flare. I gained more doing this rather than using pvc, as seen in the spl gains thread on here. But that did gain me a few tenths though and look prettier with duct tape. But anyways.
How is the speaker wires ran through the box? Use bolts, just don't use those terminal things, never had much luck with them. Or just do a smal hole and run the wires through it and caulk it. And I would run another metal thread between the subs.
Then, box placement, I gained a whole db in my suv doing sub and port up. So if you can move that box, turn it over, subs up, port firing up on the driver side. Good luck!