I hope to do the story and then get the Killer App mod, or should I just install that asap?
You can install it right away. It doesn't make any significant changes to the Single Player game. (The changes are mainly in Multiplayer.) The mod just fixes some things, adds a few minor graphical touches, some optional new cheats, and widescreen support. If you install it later, you won't be able to load any of your saved games any more unless you disable the mod.
Be sure to watch the video in the first post of the KA Mod topic
to ensure a smooth installation.
Congrats on scoring a copy of 2.0. It's getting hard to find at a reasonable price. People are price-gouging because Tron is popular again right now. That's why Disney should really release it on GOG.com.