There are easy ways and hard ways to do everything. I prefer the easy way, but i know from experience that some prefer to take the road less travelled.
Q. Can you fly with a bent main shaft?
A. Maybe, but it will vibrate horribly and probably knock out the gyro and/or cause other mechanical failures making another crash almost certain.
Q. Can I use a 4S battery on a 3S 3500kV motor?
A. Possibly but you would need use very low gearing, even with lower gearing it's quite likely you would burn out the motor and/or ESC. The ESC would have to be 4S capable too.
Q. Can i use a 4S battery on a 1800Kv 6S motor?
A. Yes but it would be way down on headspeed, high gearing would get some of the lost RPM back but still not a good option.
Q. Can i make a 4S battery out of two 2S batteries?
A. Yes if you make a series wiring harness, but the battery and wiring may to be too bulky to fit under the canopy. Also depends on what mAh size of battery you are talking about.
The easy option is just to use a straight main shaft and use the correct battery for the chosen motor.