I would definitely invest in charge pipe first. It's known to fail even under stock conditions. No point risking being stuck on the side of the road and without a car over a couple hundred bucks IMO.
I run a jb4 since my warranty expired a couple months ago. So can't really help you out with a warranty friendly tune advice. I haven't had any issues with jb4 and it has alot of cool features along with solid performance gains.
Good luck.
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