Wiring Ignitor to correct Coilpacks - Need clarifying

[2plus4plus0eq6]

I started my car a couple weeks ago to see if I wired everything up right, but now I am having doubts if I wired my Q45 ingitor chip properly to my coil packs.

My car starts, but its a little rough. I am thinking its because the engine has been sitting for months (s14 SR20DET).

I followed the directions from here:
http://srownersclub.com/faq/faq_ignitor.asp

In the directions it says the following:

Pin 1 --> Coilpack 1 (Red)
Pin 2 --> Coilpack 2 (Red/Green)
Pin 3 --> Coilpack 3 (Red/Blue)
Pin 4 --> Coilpack 4 (Red/White)

Now my questions are:
How do I know if I wired this correct?
Am I misfiring? If so, how can I tell?

From the pictures below, you can see that I marked my coilpacks with numbers to indicated which coilpack is what. I just noticed that the coilpacks and the plugs have already been marked with dots to indicated which is which from the previous owner.

Are coilpacks 1 through 4 layed out in sequence 1, 2, 3, 4 or are they layed out 3, 4, 1, 2 like I thought they were. I am thinking 1, 2, 3, 4 because thats what the FSM says - Pages EL-264 and EC-121. Does this mean that Heavythrottle's wiring is wrong or maybe its for the s13 SR20DET?

I am really confused. Not sure If I explained myself clear enough. If I didn't, please let me know. Thanks