You'll defintaly have to re-jet, the stock exhaust traps exhuast gases longer so it can be burned off turning carbon monoxide into carbon dioxied, there fore a leaner condition runs fine but at a huge power loss. when you put a new exhaust on your increasing the fuel/air flow into the engine, therefore needing more fuel to burn at the proper fuel/air ratio

in higher altitudes you have less air so your fuel/air ratio changes forcing you to lean you fuel out to run better at high altitudes hence 14.7 parts air to 1 part fuel