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I just pulled the jack/tool cover behind the rear seat. Seems there is approx 6 1/2 x 10 x vehicle width (didn't measure because didn't think it would matter as you could 3-4 batteries wide). So how about a sealed battery or multiple even in that location? With a little work I think it could even remain hidden and flat with the rest of the seats when folded, and stock tool storage shouldn't be an issue.
There are plenty of spaces to mount it like I don't run a spare in the stock location so something can be made to house it there. But you have to keep in mind that cooper prices are way up and the cables needed if the battery will be asked to start your jeep won't be cheap at all. If all your going to do is run accessories then the cables will be a little cheaper. So keep the cost of parts in mind while planning this out. I will be doing mine as soon as I get my wife a new battery I will use her old one to do the mod
Where are you planning to put yours? Spare tire area? Isolator? What size wire?
I'm putting mine where the stock intake sits. The wire needed to run cranking juice or winch use is like 2 or 3 gauge I think can't remember off hand.
I'm going to go get my wifes new battery today. As long as I can find one and don't have to order it online I'll probably start mounting the second battery under the hood today. I hoping to at least get the battery mounted today at least then worry about wiring it up later.