What voltage are you expecting from your stepper motors?
Who or what is going to turn them for several hours to charge the battery?
Your MC34063 circuit produces 12 volts, if you are using that to charge the 12v battery it will not work.
You will need more than 12v, how much more depends on the battery chemistry. (And dont forget about the voltage drop across diode D1).
Why are you using a 12 volt battery when you only need 5 volts?
What is the purpose of the BC548 and LED1 ?
If it is supposed to be a charge state indicatot for the 12v battery, it will not work well.
What is the TIP127 circuit supposed to be doing? (Apart from wasting energy as heat).
Do you really need those resistors on the D+ and D- pins of the USB connector?
So, you have some stepper motors whirring away and a voltage converter circuit to charge a 12v battery.
You then have a regulator (7805) and some other odd circuit (TP127) which are dissipating more than 2.4 times (12/5) the energy that you put into the phone battery.
No wonder the TIP and the 7805 are getting hot.
Are the TIP and 7805 mounted on heat sinks?
You may want to re-think this circuit.
JimB