Alright now I can help you out a bit. Head unit I would look at a kenwood 6140 or if you are trying to keep your nav in tack get something like a alpine 9886 single din head unit. This will help you out very much as the bose system will be totally bypassed and you can start fresh.
Speakers
For what you like I am the same way a bit of everything. I would look at either a set of Image Dyanmics CTX 6.5 components.
CTX65CS - Image Dynamics 6.5" Component Speaker System
Or a set of Rainbow SLC's
SLC 265.25 NG - Rainbow SLC NG 6.5" 2-Way Component System
Both will give you clear sound for what you listen to.
Sub now if you are looking for a budget sub look at this kicker vx
06CVX10-4 - Kicker Comp VX 10" 1200 Watt Dual 4 Ohm DVC Subwoofer
If you want something a bit more SQ than I recommend the Image Dynamics Q sub
IDQ10V3.D4 - Image Dynamics 10" IDQ Version 3 Subwoofer
The sub box I highly recommend the Z enclosure as it works and fits very well.
Amp
There are a few ways you can go about this the best way is a small alpine 5 channel amp for everything.
PDX-5 - Alpine 5 Ch 600 Watt Digital Power Amplifier PDX5
Or you COULD run the speakers off the head unit but they would sound better with an amp.
And than run your sub off a amp such as this
T500-1BD - Rockford Fosgate Power Series Mono Amplifier
As far as wires you will need a kicker hyperflex 4 gauge wire and stinger rca wires also speaker wire you do not need anything thicker than 16 or 14 gauge, except a small piece of 12 gauge for the sub.
http://www.amazon.com/Kicker-05PK4-4...1748527&sr=8-2
http://www.amazon.com/Stinger-Pro-Ch...1748556&sr=1-3