I could be wrong but it sounds like your cylinders are fighting eachother. Have you checked your float heights to ensure that they are the same height and also to the correct height? I had messed with mine on my 500 and had the floats at diff heights and at idle it was pretty rough, once I adjusted them to the correct height it idled much better. This could also explain some cylinders being hotter than others, the ones getting more fuel will be hotter than the ones being starved (I think, could be reversed.)
Also, if you haven't vacuum synced your carbs during a tune up that could also be a cause.
Are 3 and 4 getting warm at least? It didn't sound to me like you were only running on 3 cylinders, as I've also experienced this, and it is extremely rough at low rpms.
HTH,
Brandon