You guys do know that the polarity on the speakers doesn't matter as long as both speakers are wired the same way right?
By this I mean, if the positive and negative are wired "backwards" (because that's the way the speaker adapters came), as long as both the left and right sides are wired the same (which they would be if both wiring adapters for the left and right are the same), they won't be out of phase and it won't matter.
If, on the other hand, the speaker on the left is wired one way, and the one on the right is wired opposite, they will be out of phase (one speaker will drive outwards, while the other is going inwards), and one side will partially cancel the other out.
Does anyone know if the original speakers are 2 ohms or 4 ohms? If the originals are 2 ohms and you are replacing them with 4 ohm speakers, the stock amp will only be able to drive roughly half the wattage into the 4ohm speakers. That will definitely affect the volume you can get out of them. It doesn't mean the stock amp is terribly weak, it's just not designed to drive 4 ohm speakers.
Has anyone tried running new wiring into the doors (through the existing conduit and connector)? I'd love to run new wire all the way to the door speakers, but I'm a bit worried about the amount of trouble running wires could be.