Changing the Heaglight, tailight or any other light will not effect your warranty. Try to stay within the range of the recommended wattage/voltage and you will never have any problems. Dont buy the NOKYA PURPLE bulbs cause they are piece of crap.
About the speaker, Iam pretty sure you have 2 rear speakers, either they are removed or blown, but the wiring should be there because your Headunit has 4 outputs on DX and 6 on EX models.
Changing the speakers is a piece of cake. Just Pry out the plastic covers on top of them. Unscrew the factory screw, put your new speakers and put new screws, you are set to go. Make sure they are 6x9.

I just upgraded mine to 240W Pioneer with 80W RMS and they sound great, but I have an EX with a 6 disc changer so I dont know if they will sound good with yours. Good luck.