The aircleaner that comes stock with your bike is the Ventilator from the accessory catalog. It is a "high flow" air cleaner, and you don't need to change it unless you just want to. The only thing H-D sells that flows any better, to the best of my knowledge, is the Heavy Breather.
If you aren't into ticking off the neighbors, I'd suggest you opt for the "quiet" baffle on the FatCat. It's not all that much quieter, but the wrap on the baffle does cut the sharper edges off the sound. If you're into stealth, like sneaking home from the club at 3:00 am, I don't think even the quiet baffle will help. D&D has a well earned reputation for excellent fit and finish, among the best in the industry.
As for the tuning device, do you have any plans to actually use it yourself, or do you intend to let someone else tune the bike? If you aren't the hands-on type, you need to first find a reputable tuner and then let him help you decide on the device. Sort of the way you go about getting a knee replacement; find the surgeon first. If you like to play with this stuff yourself, the TTS MasterTune seems to offer more capability than the H-D SEST (it's the same company that originally designed and provided the old SERT for Harley). These "devices" are really just software and a communication interface that allows someone to change the settings in the stock ECM. One nice thing about the TTS system is that it lets you save the stock map, so you could revert to stock without leaving a trace if a warranty issue were to come up. Unless something has changed recently, that hasn't been the case with the SERT/SEST.
BTW, if your dealer is just trying to sell you the SEST and a canned map instead of a custom dyno tune, I'd pass on that offer.
Jerry