Welcome Tony! Sadly, I will ask you delete some of your current mods to help the engine. It's good that you changed the plugs, but E3 does not have a good reputation. Stick with Motorcraft or NGK, they work very well. And be ready to change plugs on a tuned engine more frequently than stock, because the plugs will get used up much faster (think 25-30K).
Delete the Superchips tuner. UGH. These types of "tuners" make it look like they make the car go faster, but you need a REAL tuning device to make it go faster correctly and safely. For example, an SCT X3/X4 or a MyCal are currently your best options. With tunes loaded, they can run up to $600 new. But this is the most significant and worthwhile investment (next to having your maintenance up to date of course).
Muffler delete and CAI are fine.
Power per mod - a rough idea:
http://www.ecoboostperformanceforum.com/index.php/topic,808
Maintenance needs include the drivetrain primarily - transmission, PTU/PTO, and RDU. PTU first, trans second, RDU last in order of major concerns. A coolant and brake flush are always advisable. Run quality oil/filter, at a minimum as specified by the owner's manual.