this would be something that you would need to be more specific about. what kind of mods are you thinking about? typically, modifying a motorcycle can be done in more ways i can think of. from simply removing the plastics, and adding a slip on, to custom builds that are done from the ground up.
modifying a motorcycle will have an impact on the performance of the bike. changing the geometry of the forks for example, can increase, or decrease the turning radius, as well as change the suspension characteristics of the front end. or increasing the amount of airflow with upgraded intake, exhaust, jetting etc... to see gains in hp, and torque.
some mods come at a price. like chopping the tail, and eliminating the rear seat. you will lose some weight, but you also lose the option of added luggage, or a passenger. frame extensions will widen your turning radius, and will change the way the bike handles. i have not ridden a bike with a longer swingarm. i think it would hurt the bikes handling.
as far as difficulty, again, it depends on your experience with mechanical tasks, and knowledge of engines, and motorcycles. i think things like different bars, fairing removal/swap, and external engine mods are easier than tasks like painting, chopping, bobing, ratting, etc... i would hope that if you arent confident in doing even the easier mods you find a friend that has some practical knowledge of mc's, and get them to help, or at least look over your shoulder.
i hope this helps.