Oddly enough all the things you mentioned could in pretty much no way have any effect on your problem.
However, after siting for a long period of time, the oil in the engine cools. Cool oil becomes thicker( the oil also settles into the bottom of the engine). When you start up your engine, your engine has a small lack of oil. That will cause rougher running.
And even once the engine has oil, it is still thicker then what would be best, so it runs a little rougher.
It may also be due to wearing engine mounts