I put a set in my Mxz 700 and they are great, but not night and day different, just good throttle response. There should be 4 peddles w/ 2 or 4 holes in them and 4 smaller peddles. The smaller ones are the covers, basically , for the holes. Thats the "two" stage they're talking about. The small ones open first then the larger ones. The large ones go on first and the small ones go on over them.
The directions say you
may need to go down 1-3 jet sizes on the mains. I experienced a lean condition when I went down two. I went back to stock and I'm ok now. So it depends on the sled. Look at the color after a run or 3 and go from there.
As for the piston check for air leaks. Did it burn down after installing the reeds? If you installed the large reeds w/ the holes in them and not the smaller covers you leaned it out beyond what can be explained!!!!!
Please tell me you did not do that. 
If you did, do not even start the sled again untill you put on the small ones!!!
I do have a bit of a smokey idle so I may go down a size or half on the pilots. Pilots only come into play from idle to 1/4 throttle and play a small role at WOT. Don't jet unless you know what you're doing, please!
This is what the Boyesen site states.....
> Secondary Reed
(Top Reed)
The top reed is specially shaped, lightweight and resilient for crisp throttle response at partial throttle or low RPMs.
> Primary Reed
(Bottom Reed)
The bottom reed is thicker, stiffer and ported to provide stability, maximum flow and horsepower at high RPMs