Just want someone to confirm that I should be looking straight down from the top when I align the pin and the color marks. Thanks!

 

Yes

 

Well, you really have to look down on the pin/pulley to see thm so it doesn't really matter if you are a few degrees off vertical. The difference will be insignificant since the pin is so close to the pulley. Just find a position above the pulley/pin where you can get a clear view.

 

Another question: If my timing was off before, is it normal for idle rpm to go up after setting the right timing?

 

try to adjust the tps