new piston

i take it that your melt down was bad enough to requier the oversizing? if so then i have heard of ppl just doing the one and not having any problems. i would try and research this a little more try and find something by Kevin Camron, hes been a 2 stroke guru for ages. you would think that the slight difference in weight of a piston a few thou bigger wouldnt be enough to cause any serious vibration issues, but i would read into it a little further. might be able to save you some mula.

It should be fine, even oversized. Although it's not the ideal case, I blew up my friends old SRV 540 a few years back, then he put in 1 oversized piston and just left the other one in it, no vibration problems, and still runs just fine today. The only concern would be premature crank bearing failure due to the vibrations, but I don't foresee it being a problem.

I also have replaced each of the pistons on my polaris 650, one by one. I wish I would have done them all, within about 1500 miles, I replaced all three pistons. How did it blow in the first place? Overheating, excessive RPM, fatigue?

I did'nt read anything in your post about boring it out.
Piston do actually wear out. Heating and cooling cycles weaken the piston and the ring groves do wear. In a perfect world you would replace all three, especially given the age, but it is not mandatory. If it is factory pistons in it put a factory one back in. Cast and forged pistons very too much in weight to mix them up.