^^^
thats pretty much what i do, this car was my first stick i knew how to drive stick, but wasnt super good at it before i got this car. i know exactly what your talking about with the 1-2 buck.
i have the TRZ mount and that helped some, but if im not paying attention i still get the jerk. i am planning on getting the new TRZ side/tranny mount soon and will let you know if that helps too.
i try to shift into second earlier then for other gears about 2500 for me.
on your question about skipping gears, that seems fine for daily slow driving. when im lazy i'll shift 1-3-5, i usually wait a little longer to shift for this, about 3300 RPM, but its not gonna hurt the car, you just wont get as much acceleration, but in the city who cares.