OK, so now I need say more

.
Two main issues and one whine:
1) When I dip a white paper towel into the coolant to see what color it stains the paper towel, it stains it orange. When I just look at the coolant in a clear milk gallon, it looks green. What is going on here? It is sludging up, (as shown in the above picture), so I assume it is Dexcool. Why does it look green?
2) I have not emptied the coolant resevoir, but have done everything else according to the FSM and yet everything does not seem to be going right. I have only managed to drain ~3 quarts, even though the whole system is supposed to hold close to 12 quarts. I can see about four quarts in the reservoir, but that still leaves me missing ~5 quarts... where is it?
Two things of note (at least to me) are that I did not get even one drop out of the block drain when I popped it out and that I have the two lines that run in and out of the throttle body plugged up with bolts (thereby disrupting the coolant circuit). Could either one of these be a clue? I certainly feel like I should be getting a bunch of coolant out of the block drain. The car was not overheating even a little bit before, so I assume that there is no major blockage holding back 5 quarts of coolant.
3) I can't remember what the whine is anymore. Must not be that big a deal.