Good power can be had from the PE by simply using a good alloy muffler, set timing correctly, increase main jet size to suit muffler if required.
if you strip the top end, match all the ports to the base gasket carefully and clean out any dags and knife edge any bridges.
if you split the cases, match each transfer carefully to the barrel / base gasket and this will assist the motor to run as best as possible before actually altering the ports if your chasing more go.
as boyd 40 said if you raise the exhaust port, you will lift the revs that the power will hit at and it will hit harder.
a larger carby may also give more top end but you could loose midrange.
The PE will give a strong powerband, not as hard as the RM but much easier to ride IMHO
you need to decide if your building a competitive mount or a drag it out and ride it for fun bike.
once the timing jetting and muffler are right, money spent on forks and quality shox will see better lap times