I'd like to get the back part of my mould painted, but I've no idea how to get a smooth finish on that side of it (the peel ply side) Do I sand it down? Brush another layer of resin?

There multiple ways:

1) sand and lacquer.  This is how I'd do it for a one off

2) remould using a vac bag rather than infuse and be very careful laying in non-perforated release film (should give a smooth finish)

3) Make two mouldings and bond them together (could be tricky)

4) as suggested above mould each side and use a closed mould system