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Thanks to Bigmav for the information and photo's here, he posted this in his build thread but I thought it deserved a thread on its own which will also make it easier for others to find.
After spending some time trying to fix the aircon up (its starting to get bloody hot up here) I found that my problem was an electrical gremlin in the fuse box. I have had some issues with the fuse box for ages but never did anything about it because I knew it was going to be difficult and time consuming but I finally decided that now was the time. The problem lies with the contacts that the blade fuses slide into, on numerous circuit the contacts have cracked causing high resistance and leading to massive voltage drops and loss of power completely sometimes. I temporary fix the problems as they came up on the go by bending the legs of the fuses to make a better contact.
You can see here the kind of crack in the fuse box I'm talking about where the arrow is. yes it took a while to find this was the problem.
And again here the terminal was completely broken and you can see the heat damage where I've circled.