Maruti Wagon R stereo system

Hi all,
well i'm from india and to be honest the installers here dont know a thing about installing a car system.I recently purchased the following items.
A)pioneer DEH-P5750MP(cd reciever)
B)my speakers are pioneer TS-A6990S (speaker 6990)
C)my sub is a 305c (305c woofer)
my amplifier is a 4 channel one.its 3600 watts amp by "sound barrier" with the following feat/specs
1)max 4x 100 watts x 4 ohms.
2)max 5 x 300 watts into 2 ohms.
3)bridged 2x 600 watts into 4 ohms.
4)pwm mosfet power supply.
5)seperate bass and treble controls upto 12 dbs adjustment.
6)12 dbs adjusttable crossover network.
7)line output for amplifier daisy chaining.
8)class ab operation.

although i have a box in my car wagon R but i dont know its measurements either.


the woofer is placed on top and the speakers are below(does this in any way effect the output of the sound.)and there is no partition b/w the woofer and the speakers.There are vent on both the left as well as right side of the box,there is also heatlone(used in air conditioners,sound profing material.) fixed on the inner surface of the box.In the manual of the woofer it says that best used in a 30 ltr enclosure with no partition b/w the woofer and the speaker.The hight of the entire box is approximately 18"withe the speakers at a height of 16".I will try and click pictures of the box and upload it in this topic.Mean while if you need any measurement of the box kindly tell me ,so that i can do that for you.

here are my problems..
1)on medium volume one can hear wiered sounds such as vibration of the rare windscreen.
2)The output of my car is loud but the entire car vibrates therefore giving a humming to the sound.
3)There is loudness without a doubt but the depth of the sound is not as good as it should be with the above mentioned configuration.


kindly help me out wiht my system as being a 20 yr old i blew most that i earned on a good sound system but unfortunately am still not satsfied with it.
thanks in advance.
cheers

so the speakers are attached to the subwoofer box? i'm pretty sure you do not want this. the speakers should be mounted in the spots within the cabin of the car. the subwoofer should be by itself. by looking at your drawing it also looks like the basket of the woofer (the pyramid looking thing) is sticking out of the box. from my experience (it's not as much as many people on this board) but i think it should be inside the box.

It's not outside the box.The entire thing is in one piece.
I beleive this is a band pass design there the woofer and the speakers share the box.
wagon R does not have a cabnet in the trunk,there is no seperate trunk.there is just boot behind the rear seat which one can access while sitting on the back seat(if this is making any sense.).