So those are two 12V batteries in parallel. No way just rotating them 180 is gonna work but I suppose you can try it.
Shunt should go in that compartment someplace making sure you only have one side going to the battery and all other negs connected to the other side of the shunt (but you already know that). If you try to rearrange those batteries the solution to the shunt problem might present itself. I can't really tell where the wires are going to once they leave the batteries. It looks like there is a bit of space around them... Hopefully enough! You will probably need another black cable to connect to the shunt...
Just thought I'd weigh in as nobody else had...
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