Hey AC_Schnitzel,
first of all get workshop manual for your model and read it.
No reason to repeat here what has already written there.
Anyway piston of the head side you are removing need to be close to TDC,
compression stroke.
Reason is to have both valve closed and so not any load on the system.
No problem to rotate engine in 5th with both spark plug removed.
According to miles on your bike can be wise to check if valve are properly sealing.
Fill combustion chamber with petrol and send compressed air stream trough ducts; check for bubbles.
If in spec. for flatness no need for machining.
According to all that and the condition of cylinder you will decide if do the same job on the front.
Of course you will have a look on conrod bearing condition.
Have a good work