Have you tried experimenting with the manual shift mode? You can wait until rpms are higher before shifting, resulting in less torque lost from before to after the shift.
I agree with all these posts. I think it all depends what you are looking for and how much you are willing to spend, of course.
The Transgo Shift kit is $250 + install. Most valve body upgrades are in the $800 + install range. Both will move you closer to a performance feel in different ways.
Reading through the lines, you are looking for better output and performance from your FX, not just the transmission and TCU? Maybe make it sportier?
Best path to follow IMO is to make all the physical modifications you plan to make and then get the car tuned on a dyno. The combination of performance parts plus a tune that is tailored to take advantage of the very specific characteristics of your setup. A reputable shop that has experience with your engine is key.
There are a couple options for this - one is a willing dealership (good luck with that one). Turbocad mentioned TS (Technosquare) and there is also UpRev Osiris. These are companies/software platforms that allow re-flashing of the factory ECU. Many shops would use UpRev Osiris to tune both stock and modified engines. I was told that even a custom turbo setup could be tuned on the factory ECU.