Spend some time reading the engine management forum, especially the FAQ stickies. Ecutek and AP are essentially the same thing. Personally I think the AP makes ten times more sense, and is cheaper in the short and long term. The software the tuner uses may work slightly different, but they're still changing essentially the same maps in your ECU.
Isn't the Baja a 2.5L? Does it not come with a catless uppipe from the factory?