is it worth upgrading to bose? (S3 8L chassis) and how easy is it? what do i need?

Just a heads up. I've noticed that on my BOSE system in a B5 A4, the bass tails off at anything above 25ish on an alpine HU, may well be the amp limiting the output or the sub cant handle it...
 
It's a lot of work.
You need to change all the speakers and rewire them back to the boot.
You need the Bose sub and wiring loom
You need the Bose amp and wiring loom.
Both looms need to be wired back to the HU along with the 2 power feeds
You will then have a system that sounds slightly better than the non Bose.
Bose in the 8L is really poor, you'd be far better off going with a stealth sub or normal boot hogger and swapping the HU (which you will have to do reagardless if the CD player is duff.