Ok, so i'm grasping at straws here;
I don't remember what I did to cause the start of this issue.
I have tried Old, new and different battery types.
However they all flatten at what seems a random rate. Sometimes it's five minute, other times it's 30 seconds.
I have opened up the loom 3 times now and stripped everything I didn't need out of it.
I simply cannot find the issue and have no idea what is happening.
Anybody else experienced this kind of problem before?

You have a total loss ignition system on a track bike? What "things" are still connected to the loom?

No need to grasp at straws.

When did this start? Since converting to total loss or beforehand?

If you've already ruled out bad batteries then there is some serious fault somewhere to drain a battery that much. To drain in 30 seconds I would be expecting smoke or fire. Have you taken the battery voltages before / after to confirm it really is a dead battery and not just a bad connection(s) somewhere that appear to give you a dead battery type symtoms?

Since there are many ways to convert to total loss what did you do to your bike exactly and did you rewire anything like the on / off switch to the kill button etc.