OK, so I recently started modding my JK, {13 4 dr rubicon} and I bought all the parts but only installed a few things so far...
1 shift knobs thought it was going to be really easy actually the hardest thing I did so far, had to cut the stock shaft down, the stock knobs are tough to remove, and the set screws on the knew knobs were really tough to tighten in at the angle my knobs ended up...
2- remote starter that works with stock remote, 2nd easiest, bought it on amazon for $115 shipped, took 10 minutes to install and works AWESOME, wish I did this a long time ago...
3- the exhaust, I bought the gibson Black stainless with metal mulisha tips, the install was SUPER easy {under 100 minutes, lol} and the sound is awesome, I have a hard top so inside its not super loud, and I dont rev my automatic jeep up much so I don't get it screaming, but the sound at idle and normal driving conditions is SUPER NICE...
I havent reprogrammed yet {I have to pick and buy a programmer}, but I have not noticed anything different in the driving power or gas usage since I installed the exhaust.
So for your questions, power and mpg so far not affected positive or negative, no codes, and as far as warranty I can not see why you couldnt just install your stock pipe back on if you were worried about an issue.
I have never heard anyone have a warranty issue by adding aftermarket exhaust, II did headers back on my z06, added an aftermarket throttle body, aftermarket clutch, ignition control, etc spent $20K on upgrades and then the car spun a bearing, covered under warranty with out an issue, then there was a top end noise, again covered under warranty no issues at all... That car was awesome as was the engine I am surprised it held together at all, had 16K miles on it 1/4 at a time...