Stock TB/Plenum are decent for the PI intake, they are something to consider after you do the swap, but aren't that big of a bottleneck IMO. The next largest bottleneck on the engine will be the headers/exhaust I think, although for people like me not willing to go through the hassle to get longtubes installed...Midpipes and catbacks are the extent of what you can do.
The ONLY way you should adjust your auto tranny is with a J-mod. Increasing pressure via tuner or anything like that will destroy the tranny earlier, a J-mod will not only do the same thing more effectively but will also extend tranny life due to reduced wear between shifts. A tranny cooler is a good thing to have installed too.