Some guys trim the bottom of the intake side skirt because it doesn't quite clear the port.
I tried it but it affects the port timing and loses torque.
If you use a reed valve, you have to cut a hole in the piston skirt to gain full advantage of the reed.
I've decked cylinders and heads to change timing and increase compression, it works.
Compression helps low rpm torque at the expense of engine longevity. Be careful here.
Raising the ports (by decking and adding more basegaskets) gives more rpm and top power at the expense mid- torque.
Longer rods improve the rod/stroke ratio and reduce piston side loading. Improves high rpm power.
The only loss is if the rod is heavier, and it usually is...
Boring is not possible unless you want to re-plate ($250) or re-sleeve ($250) the engine.
An odd sized piston is worth more than a new engine.
The real gains are:
1) Improved combustion chamber shape. 2-3mm squish band, 0.7mm squish.
2) More rpm. HP=RPM x Torque so raise RPM = more HP. Generally about port timing.
3) More torque, generally done by better cylinder filling. Open ports at the bottleneck.
4) Tuned exhaust pipe. Big gain if the tuning is right.
5) Perfect jetting and timing. Both have to be adjusted for the motor.