well, im sure you know that there are extreme differences between your 5AT and a 6MT........basically, a down and dirty description:
the manual transmission has a set of gears on a selected number of shafts, usually 2, which are the main shaft and counter shaft. You control which gears are being used based on where you locate the shifter (it is alot more in depth than that, cause you have sycros, all types of bearings, idler gears, etc....but thats pretty basic).
in an automatic transmission, there is a whole new world of complicated stuff. The v/b or "valve body" is something that every automatic transmission has. Basically imagine a maze with lots and lots of little channels spread all throughout it. Well, basically, this is what your valve body is, along with alot of springs and shockingly enough VALVES!!
When you are driving, your automatic transmission is doing alot of work based on what your foot is doing. for instance, if your driving and decide to give it WOT (wide open throttle), your transmission will downshift to the necessary gear, usually one gear below what you are in. Or just driving regular, your transmission bases your speed, the throttle posistion, etc...on where it needs to be to properly shift and to be in the proper gear. And for all of this to happen, you need a good valve body. Basically hydraulic or transmission fluid is routed through this maze of channels i was telling you about, and based on what you do with the gas pedal and gear shifter bases where this fluid goes and activates the proper gear. the vlave body controls how smooth your tranny shifts and everything like that.
What they mean by upgrading your v/b they mean basically getting one that is already upgraded or having yours sent in to be upgraded and sent back for you to reinstall. They will usually port the channels and install better/stiffer springs into it so it will handle more power and shift smoother with this added power. With a SC or TT setup, this is probably a pretty wise idea. It will prolly be expensive, but if you plan on spending 10k, you may be able to afford it.
A tranny cooler is important to and relatively inexpensive. It simply keeps your transmission more cool, and with added power being introduced to it, it is real important to keep it running as efficent as possible. When metal heats, it breaks easier, so keeping your transmission cool with the power that any FI will give you is pretty key.
the toque converter is what acts like an manual transmissions clutch, except it is controlled by hydraulic fluid. ive never seen anyone upgrade a torque converter, but im guessing they are just stronger.
i hope this helps