is your ion 3 an automatic? if yes, then you'll need the F35 tranny from an 04 (04's have different motor mounts than 05+)
i believe that the 2004 uses a different ecm that has not been unlocked as of yet by HP Tuners, so you would either need an LSJ pcm or some kind of trifecta tuning.
it is very possible to do this, however it might be more trouble than its worth. if you can find a cheap used LSJ, and are competent enough to do it yourself, then why not?
some people just buy the supercharger setup (supercharger, intake manifold, alternator, belt system, intercooler system) and retro-fit it to the 2.2L. that might be a better, and cheaper alternative. then all you need to worry about is tuning. like i said above, i don't think hpt has unlocked any ion that was not a redline, so you'd have to PM vince at trifecta.