There's no clear and easy answer to this. Every bike, every person and every mod is different. Bikes are built to a cost and when they're built, corners are cut to save money. As a rule, if you're modifications and upgrades address the cuts costs then they'll improve the bike but otherwise they tend to do the opposite. I also feel that in most cases, removal of unnecessary restrictions such as emission controls will serve to make an improvement without a loss in reliability. My bike is heavily modified but highly reliable because I addressed the design issues such as overly restrictive airflow, lousy shocks and poor lights. Other people using the same model are talking about booster plugs to over-ride the ignition, that run contrary to making the bike reliable, in my opinion.
My brother bought a KTM 690 from new and modded it lightly with a new exhaust and some other parts. It never ran properly after that and he ended up giving up on it. Once returned to stock it ran fine... although it still leaked oil and needed a new engine.
Modding the bike is a lot of fun but it needs to be done intelligently. You don't really need to understand what you're doing as much as understand the consequences of what you're doing.