I'm just ordering some electrical bits to start the wiring on my J15 over xmas and Im not sure what cable thickness (or rating) to use for the cable that will take power from the alternator to power everything else in the car.
The power from the battery to the starter then alternator is fine as I have the donor cable.
I'm just not sure what amps I could expect for the feed from the alternator to the fusebox and then the split for ignition and non ignition feed.
There arent many electrical bits on a J15 so just lights/horn/ECU/fuel pump etc.

Depends on the alternator rating which could be anywhere from 35 to 120 amps.
A lot of older alternators used two main cables.

There are a number of ways of doing the the alternator main connection, (1) simplest is straight to the battery connection on the starter solenoid or (2) you can go straight to the battery or (3) straight to the fuse box.

With (2) and (3) you have the option of putting a Midi or Maxi fuse holder in line with fuse rated at say 80 to 120 amps in it you can then use the Maxi/Midi fuse as the split point for ignition and permanently live loads.

Modern wiring has thin high temperature insulation which can run hotter allowing cables to have a higher rating for the same cross section.

Check out the wiring loom manufacturers sites.

Also keep runs to a minimum - it saves money and weight. Think about relocating high consumption items as close together as possible. i.e. put the battery next to the starter (or use a supercapacitor as a buffer).

Using led's cuts the cable size dramatically to the point where you can use signal wire.

Of course there are all sorts of compromises and there may be some who disagree

Cheers!

Using the Puma or similar battery fuse box saved me a lot of thinking as it takes care of all the high current items like fans, fuel pump and the like.

http://sylvabuild.blogspot.co.uk/2012/09/the-wiring-and-dashboard-design.html

In the case of the loom I made up my own harness jig and made my own loom before installing it in the chassis. Still got the cct diagram and some of the information if it would help you.

This one is a bit out of date but gives you the idea:

http://www.alastair-reynolds.pwp.blueyonder.co.uk/Sylva/proposed%20wiring.pdf

I found the 7 style harnesses did not adapt well to a mid engine car so did my own however it was a poo load of work, probably one of the most time consuming parts of the build.

The Puma battery fuse box sits nicely into the near side sill cover.

Online calculators that may help.
https://www.google.co.uk/?gws_rd=cr&ei=4ACuUoDaJuLK0QWm04GACA#q=thin+wall+cable+calculator
If they want a voltage drop input 2% is what I used when calculating mine.

There are also calculators for ATO blade fuses.