I've ordered alpine parts from here before when I've needed something. You can look up the price and compare it to ebay. A lot of harnesses even for the older stuff has been available on ebay lately and it cheaper the pacparts if available (I just got one for a 3527 amp).
http://www.pacparts.com/
If you are going to amplify all your speakers you can use a y-adapter for the rca input to the first amplifier for the components and then run the signal for the sub off of the sub output from that first amplifier.
It's not the most elegant or sophisticated solution. And you may run into some problems level matching the inputs between your headunit and the mini disc player but it'll work. And it's probably the cheapest solution.