There is no reason to put a tune on the engine absent accompanying mods it is set up for. You'd just waste gas for the most part.
smaller pulley = more air, on stock tune = lean AFR = Knock = bye bye engine!
you can get a boxed tune by letting Will @ Overkill know what you PLAN to do to your engine, it'll get ya close. But to realize the best performance and advantage of mods would be to In-Car tune the PCM.
3.6 pulley isn't much of a change in anything... Save your $ and make a plan. Piecing parts together haphazardly without a clear thought to what you want out of it will just lead to wasted monies as well. Like you said, you have maintenance items to take care of, do that first. Take care of all and any issues the car may have, modding with issues present will only cause even more problems.
3.6, Plog, larger maf is going to give you what? What are you after? What do you want out of engine, car? Make a plan, read, read, and read some more, then ask questions, modify plan... Save $, assemble parts for modding, then go for it.