1. Never ridden a pro circuit pipe.
2. 12/47 is a lot cheaper, uses the same chain length (108L) and you can change back to the 13T in a couple minutes. No excess wear issues with the 12T. RK usually runs about 20% less than DID. I got 2 years out of my last RK riding most every weekend of the year. Sprockets? Opinions of 'facts' differ, but I prefer steel (self-cleaning rear) over al-u-min-ium.
3. A set of .38s is probably close to correct.
4. 4.8? Maybe. IF you want the bike lower, resolve that issue before you mess with changing the spring. A longer set of pullrods will not only lower the bike, but will change the leverage angle to the shock spring with the effect of making the spring seem 'softer'. So the 5.0 may work fine for you with a longer set of pullrods. You could always wear more gear! ;)
5. Jetting is the #1 method to make your bike run the best it can...in any atmoshperic condition.
If you haven't check it out yet, read thru the excellent info on CDaves' site:
http://justkdx.dirtrider.net
Note the carb tuning article, needle decoder info and such. Your bike will
NOT reach its full potential if you don't jet it properly. ...and if it's jetted stock now, you have a LOT to gain!
Check the 'new bike prep' article. Do it now.... do it later. Problem is, if you do it LATER, it will cost you a whole lot more $$!
Cheers!