Are there any diagnostic codes stored (if you don't know how to heck them look in the FAQ section)? Roughness at startup could be any of a number of things from a misfire to a minor knock due to loose bearing tolerances (doesn't mean they're bad, just old), oiling issues, or running too rich at startup (disconnect the cold start injector next time you start up and see if the stumble goes away).
Just because you've noticed one symptom over a long period of time it's no reason to assume it's related to the sudden, new, extreme problem.
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