Well you wont be useing Transistor- Transistors.. I suspect RF Power-FETS.. Wont be super Hi power.. Hi current Low Ohms.. not very Hi a power level at all.. to-120 or to-220 cases will be all that the main switching transistors will live in (oh on a lump of aluminium)

You reference clock on the toy would need to be high enough that any adjustments would be in clock cycles advanced or retarded..

Not sure about the IR Beam... During the Proto stage it will help you check your estimate of timings. In the final build will probably not needed.. only perhaps as a calibration assit

..

hmm I thinks I need to do some math.. and and a bit more study on gauss guns..