coughing

Is she firing on all 4 cylinders when she is cold? if not, you have at least narrowed the search to that specific cylinder. Try to spray some water on the exhaust when she is cold, and see if it evaporates on all 4. Even if she is cold, and you use choke, all 4 cylinders should fire.
If there is one or more cylinders that does`nt fire, try to switch the coils, and see if the problem goes to another cylinder. If so, there is a big chance that it could be one coil thats bad. If not, it might be carb or plug. My 900 coughed like that, it started with some mild coughing, but became worse after some time.

Did the new diaphragm solve the problem?

Snow sucks

did you measure the temperature on all cylinders? if its not the same, try to swap the coils, and see if the problem changes cylinder. It sounds like coils to me.

The dealer in Norway said that they would not recommend nology, only original Gil coils, so I got an original. They could not come up with any good explanation why, so next time I`ll go for something else.
BTW, I just got my bike back from the garage, they changed oil and filter, spark plugs (yes I`m lazy this winter), changed a vacuum line and checked the valve clearance. 3 valves was to tight.
I have not tried her on the road yet, but she purrs like a cat.

You get the coils from your dealer or Nology, Triumph coils are not cheap, but I`ve never tried Nology myself. There is no trouble changing the coils yourself, just take off the fuel tank, and there they are, just be sure you change the right one, and get the wire ring right. It took me about 1 hour to change one, and I`m no mechanic.