The reason it might not be shifting into second gear is that you are missing a ball bearing in the transmission, or one of the teeth on the spur gears got chipped, which is very unlikely because they are made of steel. You should open up the car using direction in your manual and see what's wrong is it. After you have opened the transmission it will be very easy to identify what is wrong with it by just checking out all the parts of the transmission.
Now for the tuning, you should just first of all set all the needs to factory settings. After that you should just start your car and start driving it and listening to the way the motor is running. If you can hear the motor sputter, which you probably happen because 2 1/2 turns for the low and high needles is pretty lean, so you will only have to worry about richening the motor. You should only turn the needle about 1/8 of a inch at a time and you should also refer to to your engine booklet for anyother help. It will tell you how the engine reacts when it's to lean or to rich.