Alright 2 the extreme, yes you are going to have to replace everything in order to do a full upgrade. Or you can use a JL clean sweep and use the factory head unit if you wanted to. That way you could keep the jukebox. Other wise I would just do a full upgrade. Your best alternative to the jukebox is a cheap ipod that has a broken screen on ebay. Sense you will not use the screen when it is docked to the head unit there is no real reason to have one.
For the head unit I would probably start out with the Kenwood 6140 as it has proven itself time and time again that is a great head unit, with plenty to offer.
DNX6140 - Kenwood Double-Din Navigation and Multimedia DVD Receiver w/Bluetooth
Or if you are just looking for a double din and are not worried abotu some of the features like touch screen and dvd playback take a look at the alpine ixa-w404
iXA-W404 - Alpine 2-DIN 4.3-inch QVGA Touchscreen iPhone Compatible Car Reciever
Amps
Now there are so many ways and companies to choose from when it comes to amps. The sky is the limit on how much you can spend on them as well.
For both of you if you are looking for a amp that will not take up much space at all and will power everything take a look at the alpine pdx-5 channel amp
PDX-5 - Alpine 5 Ch 600 Watt Digital Power Amplifier PDX5
Or if you are looking at separate amps for speakers and subs here is a selection of ones.
SUB amp
Kicker zx500.1
ZX500.1 - Kicker 500W 1 Channel Amplifier
Polk Audio
PA600.1 - Polk Audio 1 Ch 600 Watt Amplifier
Alpine
MRP-M500 - Alpine Mono 500W subwoofer amplifier
Speaker Amps
Alpine
PDX-2.150 - Alpine 2 Ch 300 Watt Digital Power Amplifier
Focal
Solid2 - Focal 2 Ch 200 Watt Amplifier (Black)
JL
300/2 Black - JL Audio 2 Ch 300 Watt Amplifier
And my personal favorite Audison
LRX 2.150 - Audison 2 Ch 220 Watt Amplifier
Speakers
Alpine
SPR-17S - Alpine 6.5" 2 Way Component Speaker System
Same as with amps the sky is the limit. I know some peoples budgets are a little more flexible so I will post some higher end components as well.
Alpine
SPR-17S - Alpine 6.5" 2 Way Component Speaker System
Polk Audio
MM6501 - Polk Audio 6.5" Component Speaker System
Focal
165VSlim - Focal 6.5" Polyglass Shallow Component
Image Dynamics
XS-65 - Image Dynamics 6.5" 2 Way Component System
Sub
I have not yet heard from the OP about what kind of music he listens to but I will recommend a 12 inch most likely.
Image Dynaimcs
IDQ12V3.D4 - Image Dynamics 12" IDQ Version 3 Dual 4 Ohm Subwoofer
Polk Audio
SR124DVC - Polk Audio 12" 1400 Watt Dual 4 Ohm Subwoofer
If you have any questions or want more info on anything just ask. Also you do not have to get the products from the site you can order them from where you would like to buy them.