Could be that your not-so-protune isn't accounting for temperature properly. There are certain tables within the map that compensate for differing temperatures. If they're not set up properly, you can have wild variations in fueling and timing. They aren't a perfect science, but if they're set up completely wrong, it could cause some drivability as well as fuel mileage issues.
One thing is that winter is never easy on a car. Though the engines enjoy the cooler air, everything else stiffens up and hardens when it's colder. Clutch wise, I have no idea though.