Audio Systems: Stock deck or New one, wiring harnesses, factory radio

Question
So i have a 800 wat amp and 2 12" kenwoods, now i had this in my 93 mazda 626 with a kenwood deck and it hit hard... Since then i sold the car with then deck in it, and kept the amp/subs in the garage for over a year. I bought a new 07 charger and got the system installed, and its no where near the same as befor. Only difference is im using a stock deck. Does having a bought deck make a difference? Or did my system probably get messed up sitting around for so long in the garage?

Answer
A stock deck will have disadvantages over an aftermarket especially using subs on one.

I would go with new.

Do not cut the factory radio plug out of the car.

You can get all the right wiring harnesses and install kits from here http://www.metraonline.com