Probably the only thing you might have done on the wiring is to reverse polarity. Even if you did that though, it wouldn't affect the volume greatly, it just makes the bass sound a lot more dispersed.
It could be that there is leakage between the plenum in back of the driver (i.e. in the door cavity) and the interior of the car. In the same manner that having a driver all by itself produces very little sound, the leakage will allow the back side sound waves to catch up to and cancel the front side sound waves. In other words, it won't produce the great sound until everything is all buttoned up.
About the only other thing that might be is maybe metal flakes are allowing current leakage in the wires.
Of course, it could also be that the new speaker drivers just aren't nearly as efficient as the factory drivers you replaced. I don't know how to measure that since it would be very difficult to compare specs that you can't get. One clue though, would be to check the power capacity for the driver. If the new ones can handle a LOT more wattage than the old ones, then you probably have drivers that are inefficient compared to the OEM drivers.
Good luck sorting it out. You may need to just finish out the entire job and then see what you have.
Cheers,
PH