Sounds to me like it's flooding the engine by overfuelling, perhaps because your TPS realignment has gone wrong and it now thinks you're on load site 15 when actually you're on load site 0/1
What makes you think the coil packs are actually duff? Something I saw that was neat was a bank of four old spark plugs with the "nuts" welded to a steel bar which you could then ground with a jump lead. Then you can attach your four spark plug leads to your test bank and crank the engine and see what's what.
You can tell whether or not the CPS is working - the light on the emerald goes from red to green when the emerald syncs up with your chosen flywheel pattern (36-4 Rover 2 in this case). If it doesn't go and stay green during cranking (e.g. it stays red or flicks green/red) then the CPS or CPS wiring are screwed.
In my experience the Emerald is as flaky as a box of cornflakes. Keep dated backup copies of both the ECU configuration file and map files - don't assume that each and every file will be error or corruption free - never overwrite a saved file - just create a new one instead; also, just because a config and/or map can be loaded to the emerald, doesn't mean it's good. So get a golden baseline map and ECU configuration file and squirrel them away. Whenever some weird sh*t like this happens, break out the golden files and see if the problem "goes away".
Cheers,
Robin