AW11 Misfire (Diagnostic shows error 3 - ignition/ecu) help?

Recently I have been getting a varying array of misfires (Severe to minor) losing 100rpm to a quarter of the revs when cruising along (not under hard acceleration), this tripped the "check engine" light.
So I did the diagnostic check of the ecu to ascertain where the problem was coming from (Ignition, Fuel mix, or Compression) - main causes of a misfire
Using this process http://www.challoner.com/mr2/tech/diagnostics.html
it threw up an error 3 code, 

1. Ignition circuit (IGf ECU connection).
2. Igniter.
3. ECU.

   now that we know where the problem is coming from, what is the next step in trying to fix the misfire? I have had a look around for other people with misfires, but it seems to be different (if i have missed something feel free to link it if it helps) 
I was thinking spark plugs ignition leads, what else would be a common problem with the ignition system that would throw up an error message?

Thanks to all
MD 

Thanks Knightrous, ill have a look at the coil and see what we can do with it 
fingers crossed there isnt much else going on.
Also, if you know, there is a 10mm hose running from the tvis to the rocker cover, any idea what it does, ive searched and found sizing etc. but not actually what its for (its cracked and trying to figure out how important it is to replace.)
 

The only difference in the error codes is between the AW11 A and AW11 B 
http://mr2wiki.com/MKI/EngineErrorCodes kind of explains it better. 

Thanks, ill check out both options and hope its not too sinister!

Ah ok thank you, to replace it are there any precautions or can i just whip it off and chuck on a new one?  

ill look for the right one, and failing that get a generic one and see if it improves overall smoothness. 

I didnt either until things wernt matching up and I had to do some searching to figure out what was wrong!
 
Ok ill have a look and see what i may need, but the CEL comes on after the engine misfires, sometimes pretty badly and sometimes not, but it will miss, then the cel will come up, then after a while go away again, it only seems to happen when the engine is at temperature, but ill start changing over parts and see what solves it.

Thanks, im hoping it sorts out fast