IMO you are making this much more complicated than it needs to be...
step one: ditch the 4in speakers... they are probably just adding noise... especially if you are running them off of spliced inputs from the front channel with no frequency adjustments (4in speakers aren't made to replicate the same sounds as 6.5in speakers so unless you accommodate that you are probably just muddying the waters)
step two: get some good quality door / rear speakers... 2way speakers. you don't need components.
step three: get some sort of sound deadening material (cruise ebay, you don't need dynamat, but don't get something that is just like asphalt tape)
step four: get a good quality head unit. just my opinion but i HATE sony. Spend a little more here and get something good. Alpine, Kenwood (just not the $150 stuff), Pioneer have never let me down. You will probably enjoy the alpine ipod control as well.
if you want, spend a little more on the speakers so you can get some that will handle some power and sell your sub / amp (i am assuming you meant 250w mono sub amp) and get a nice 4channel amp to run all the speakers off of. You will hear a world of difference between a good head unit powering the speakers and a dedicated amp doing the job. I'd def consider selling what you have to make some money for good stuff though. You could probably have a pretty respectable setup that sounds worlds better for less than $500... even less if you can sell off what you have now to make some dough back!
sorry its late and that looks like one big run-on sentence
