Dodgy earth maybe? The crimps on the Power cables/earths been done properly? if they arent it will cause problems.
I know i ran a 0 gauge pos and neg cable to the engine bay just for good measure and as it was recommended to me, something to do with ECU's not liking reading the voltage through the chassis of the car.. or something
Have you tried rigging the battery back up in the bay and driving it for a few days and seeing if the problem resides?
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