I had a custom box made with an Eclipse 10" and pulled out the spare which I know you are not supposed to do for structural integrity but did anyway. I have Boston Acoustic Pro's all around with 4 separate crossovers for each location.
Be careful about putting enclosures on the sides, several posts have been written about blocking the rear vents and heat building up which can cause the adhesive to weaken on the hatch clasp.
Good luck, you may want to run new braided cables with high quality speakers because good speakers can really make alternator hum more noticeable. The braided cables help block the hum by an electromagnetic process. The filters placed in line really won't help much, I tried them and tore my whole system down searching for the high pitched wine only to discover it was coming from a broken ground attachment in a cable. If you have Magnecore spark plug wires you pretty much cannot get away from the hum from what I understand. I do not have them so I cannot say myself, maybe others can help.
Good luck!
Kurt