*edit* just to clarify when car is warmed up (temp need moves at least 1/4 way up) the stuttering stops...

Happens when its cold out. I have a fpgreen with bigger injectors installed a couple months back but since it just started getting cold I have had this problem.

Another problem which may or may not be related is when I boost and let off the gas, the revs stay at around 4k. Feels like a stuck throttle body. Do you guys think they are related? any advice?

 

Sounds like you have unmetered air getting pulled into your engine. Check for vaccum leaks....I doubt it's a leak pre-throttle body, but I'd check all my couplers just to be safe.

 

fluctuations in temperature causes things to shrink and expand. things like silicone couplers. I would do a boost leak test. Fixing boost leaks can typically help idle. The MAF accounts for temp changes so as long as there are no leaks the tune shouldn't be affected by the colder weather.