I would NOT put the OEM piston back in because there has also been a number of ring land failures... I've changed 3 or 4 of those as well, including my own '05 (at about 20k miles).
a rejet is not required for the 685 unless the exhaust and/or the intake is changed... mostly the exhaust. research the 22 cent mod. the KLR is lean on the bottom end, so maybe you don't need that at 5000.
it's also worth your while to do a little head work. there is a big restriction in the exhaust port....
that can go away with s bit of grinder time. even a fairly crude removal makes a difference
this pic on the intake shows a bit better.... trying to taper the approach to the guides for better flow.