Question is would it be alright for me to swap over to a different size chain pitch and different sprocket to act as the start of the second reduction?
Technically yes, you can use a different pitch set of sprockets and chains for the second stage but what is the advantage in doing that? You end up with two sets of incompatible chains that means you have to carry spares for both in the event they break. For the power of the motor, I would honestly stick to 6mm pitch for both stages to start off with.