on a stock muffler - would it be a good idea (or viable idea) to cut out the two 'cones' in the inlets to the muffler from cylinders 1 & 4? Or would it make the back pressure uneven and not be good for the engine? Or am I just being anal and wasting my energy?

Cheers

Couldnt hurt mate. Most used mufflers these bits would have been the first thing to rust away.
Getting rid of the pea shooter exhaust tips will remove restriction. Go a straight pipes or taper tips.