Our Minor is a 1958 too. Towards the end of the restoration 9 years ago, I had to address the same issue.
This link shows the use of colours in Lucas-made harnesses.
http://www.mgexperience.net/article/lucas-colours.html
I stripped off the cotton covering and made sure that I taped up anywhere in the loom where a wire 'exited', to maintain the correct layout. KEEP a sample of the original covering if you propose to get the new harness recovered.
In our car, all the original wires are plastic insulated, and apart from a few that needed small extensions/replacement, I have used all the original loom for its original purpose. If an original wire needed an extension, I cut the wire back so that the join was inside the harness for protection.
I didn't have the official list of colours at the time, so have used a selection that at least are different to any of the originals, and mainly different from each other! Most of the new wiring is 14/0.30, with 28/0.30 for lighting and other 'high power' (>60W or 5A) uses. The alternator will need at least 84/0.30 for around 40A, or bigger for a bigger alternator.
I have a 55A Lucas alternator that has two large Lucar spade terminals, so I use 2 65/0.30 cables from the alternator, which is easier than a single 120/0.30 (I do use the larger cable from the ammeter back to the battery)
I made a list of all the things that would be different/additional to the 1958 original, like heater, spot lights, alternator, flashing indicators, reverse light, rear fog, oil temeprature gauge, anti-diesel valve etc. I wanted to keep the under-bonnet appearance as tidy as possible, so made one additional hole in the bulkhead for all the new wires, and used the original hole for the original loom. Any existing joins inside the harness, and all new joins were made or re-made by soldering the wires and covering with heat shrink insulation material.
I have put the additional fuses, relays etc. all behind the drivers side glovebox (have removed the lining this side). The result is a tidy under-bonnet, and a bit of a cat's cradle behind the dash!
From the list of additions/changes I laid out each wire in turn from source of supply, fuse, terminal etc. to the point of use - adding at least 200mm each end for final termination, and making a note of the colours used each time! At this point no terminals were fitted. Once laid in, I taped the whole harness together at every exit, and the odd taping in between.
By doing it in the car, if there is a problem that the harness cannot be got out, it's a fairly simple job to make the change - the same can't be said once it's all nicely covered and it will not go into the car!
The final job was to get the whole loom re-covered, using the original flecked pattern (hence the sample), by a company in Nottingham called Autosparks, who are extremely helpful and reasonably priced.
The link to them is:
http://www.autosparks.co.uk/
The under-bonnet is shown on the picture below:
As you can see the size of the 'new' harness going through the new hole in the bulkhead, behind the remote brake fluid reservoir, is about the same as the 'original' - shows how simple life was in 1958!