Tim,
Sorry to hear you are still having problems with your missfire. As you know, I did pretty much the same conversion as you and have the following comments:
My car is very lumpy when first started from cold. I'm assuming this is because it runs rich until the lambda sensor adjusts the fuelling on the MEMS ECU.
My car does around 37pmg when touring to give you some indication on fuelling. It is also running on the 1400 fuel rail and regulator.
I'm assuming the fuelling can't be too far out as it passed a full CAT emissions MOT with the current set up, although I did chuck some injector cleaner in the fuel and made sure it was nice and hot before the test.
As I have an R300 engine, I did have to file out the inlet manifold to match the larger ports. I used a VVC inlet gasket, but it was still touch and go if I would achieve a good seal between the inlet manifold and block.
Like you, I have also fitted verniers and retimed the cams.
Have you eliminated the possibility of a leaking inlet manifold (sqirt easy start around it) or a sticky valve (compression test?)?
I don't know if I've just got used to the extra power, but I do feel as if the engine is 'breathing' a bit heavy when pushed hard. I'm assuming this is down to the restrictions running a ss plenum and standard exhaust.
I hope you get it sorted soon as I can understand your frustration. I do however feel that fitting an Emerald may mask your problem, but I'm not sure it will cure it!
All the best.
Bruce.