For minor crash repair you shouldn't need to do too much adjustment so be careful. Touching on the specifics you mentioned--

Pitch on flybar paddles is always zero relative to each other and to the frame.

Pitch on the blades should start between about -9 and +9 degrees in idle up, and for learning, between about +1 or 2 up to +9 or 10 in normal; even if you're learning, though, if you're flying outside in any amount of wind (>5mph or so), the low end should be -2 or so instead. If you're using the stock transmitter, then you don't have end point adjustments, so just adjust the low pitch in normal mode to start and ignore the others. Always disconnect the motor leads when you're messing with these adjustments so that you don't accidentally start it when you're checking travels.

The manual describes how to set up the servos and adjust the ball links; start the setup by adjusting the servo arms and lengths of the pushrods as described in the manual, then adjust individual pushrod lengths to level the swashplate, or all links together if you need to make large adjustments to rotor pitch. Tracking the blades is described (briefly) in the manual, but the description there should be sufficient.

Beyond that there is a lot of info on setting up CP helis on this board so I'd suggest some targeted searches, or take a look at bladecprepair.com-- that site is targeted toward the EFlite Blade, but the two are very similar so you can get some good insight there.