Most of the stuff youll clean out is solder flux. The rest will be machining oils and similars.
Took 4 soaks for my PA120.2, and 5 for my 120.3.
I've heard of some particularly manky Swifty MCR-QPs taking as many as 8-9.
The main problem here in not discoloration, unless youre some sort of bling-addicted pansy with windows and caths, its that the stuff that comes out of the rad will clog any small channels the coolant has to go through - for example Storm/MP-05 w. Injector plate/TDX w. Injector plate nozzles.
If you add too much additive dont be surprised to see a whiteish film forming on the tubes after some months, as the water evaps though the tubes and excess dye precipitates. Enough of that and youll be unclogging your loop again =p
Basic rules really
1) clean the inside of your rad well, it pays off on saved work down the road.
2) check the inside of block for metal shavings which could kill your pump, clean them of machining oils etc. block QA is good but stuff does slip though and they simply dont have the time to clean every block perfectly.
3) dont add too much additive for colour, 5-10% at most unless you have alu in your loop, in which case you best get that alu out of your loop pronto. add more and itll clog up even an apogee.
4) stay away from dye if at all possible. there are a few makes that dont precipitate easily but its roll of dye here (terrible pump intended).
5) dont boil your tubing, most makes' molecular structure degrades @ ~105c, so its not really safe if you live near sea level. dipping the end in water poured out of a kettle to make slipping it on barbs easyer is fine.
6) dont use chemicals on watercooling plastics, and especially organic acids (eg vinegar). clean them with distilled water and new toothbush.
follow all that and you can run a stain-free, clog-free, algae-free loop with just distilled/deionized h2o from your local supermarket and a few drops of iodine/cap of your favorite additive.