So I've searched and searched with nothing conclusive, but I'm admittedly a bad searcher... I have a sort of stock samurai 235 75 15 tires, if I upgrade to sidekick calipers and rotors will my stock master cylinder provide enough fluid for the larger piston? Most of the info I find is guys swapping to discs at the same time and then they use the Subaru or other master cylinder to work with the rear discs. I've found you can upgrade brake stuff until the cows come home but if the system is not balanced correctly it isn't of any benefit. So has anybody done ONLY the caliper rotor Swap and left the Mc stock? I think the next step would be switch to the sidekick Mc as well?

You should be fine as far as pressure is concerned.  I ran disk brakes on all 4 corners with 33's on an SJ-410 with manual brakes and didn't have a problem.

Are you having issues with brakes with that small of a tire?

No problems necessarily, I just tow a trailer much of the time and I have to replace the 260k mile calipers and the rotors anyway and contemplated upping the brake setup. I like the idea of vented rotors. Also prices seem to be cheaper on the sidekick components...

Gotcha.  Make sure you get the 4-door Sidekick parts then.  The 2-door setup is a bit smaller and is non-vented on the rotors.