Hi Brain.
The reason of choice for the bubble relay box was a guy that does bubble to turbo conversion's suggested this way. It's a neat little 4 relay box (600 box has no starter relay in the same box as the other three) and does away with the big Rover fuse and relay box. Also looking at the pictures from Marlin's turbo, they did it this way too.
I think I may of cracked it. I spoke to Marlin's Simon. The wires I have left over (Purple, Brown, Brown/Slate's and Brown/White) will need to connect to the positive terminal on the battery each with a 40A fuse. The Brown/White (Fuel Pump) will be fused with a 15A to the battery.
The green (switched), simon say's it's used to switch off MEM's but on the diagram it's permanent to engine compartment fuse box so look's like green will be left over.
Fingers crossed!