I have a Smarty Jr, it's an great programmer. Im always on the 70hp (towing) tune. Your trans should be fine on the 70hp tune as long as you don't beat on it all the time. AEM makes a pretty affordable intake. Thats what im running but I switched the AEM filter and now im running an Amsoil Nanofiber.
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2004.5,
CTD, Reg. Cab,
SLT, 4x4
off-road,
285 BFG ATs, 48RE, 4.10s,
5" TBE, 6" SS tip, AEM Dry Flow, silencer ring MIA,
Smarty Jr, Autometer, Pyro, Boost, Trans, Raptor 100