Little more than a year ago I lost the top end in a motor, The jug I ordered was for a Grubee GT 5, also the Wrist pin bearing and Piston with rings. After parts arrival and during install I noticed the cyl intake was for 40MM intake (SR Body?). OK I fixed that with a prior mis-order which included that particular intake. Now the piston was too short at the top (didn’t come to top of cylinder) and too long at the bottom (piston stops /hits flywheel). Sent me the wrong piston!! Because of this I employed what we call here in the north “Yankee Ingenuity.” Now Duane @ that’s Dax says you got a J type motor and a D type motor to this day I’m not sure which is which. Seems to me Grubee engines are one type and ALL the others are the other type. I’ll leave that to Duane, if he will please to explain the differences. So here I am hundreds of miles away with the wrong parts. In my album I have a Flying horse piston in a GT5A (SR???) Cylinder on a Grubee Engine bought thru Kings. As the photos show I had to shave the cyl top to match piston travel in that direction and trim piston skirt to clear flywheel also had to half moon on the intake side. With all that said the engine is mounted on a 24” bike has been running amazingly strong since. I’ld like to do another motor like this but to be completely honest I don’t know what ta heck I got. Check out the Flying horse piston in the GT5 album. Shows what I did. Maybe you can shed a little more light on this.
Obviously port timing is going to be wacky but if you're describing what I experienced not long ago with my new cylinder and piston, then maybe. I didn't bother modifying anything on them because the plan was to keep the piston stock, but I did notice the ports were much lower and the piston wrist was much lower too. I never used my current piston with the new cylinder either, because oddly enough the new piston sat so high above the cylinder head I had to use 3 base gaskets and 2 head gaskets just to get it to clear the head. Doing that, it ran.
Sounded like it had mad power comin out the butt, but had none at all. Insane compression, but no power. I have reeds so even if the piston didn't completely cover the intake port at BDC (which I assume it didn't), the motor would have ran fine. But at BDC with the new piston (remember it sits higher) only half-uncovers the transfer ports and the exhaust port doesn't open till the last second. So it's got a full 40mm or so to compress and fire, so again, insane compression. I *would* look into using the new cylinder with my original piston but both have reed ports cut into them and I'm afraid one would snag the other. So they're sitting here... waiting.
However if you're saying yours runs with more overall power, then I'm at a loss, perhaps the new cylinder has better port timing? Maybe the extra wide intake port helped? (you didnt mention if you ported your old one). Or if you mean you can rev higher and get significantly more top end and vibrations are reduced dramatically, thats because you lightened the piston. Less weight means less inertia, so the piston can go faster and not affect the crank momentum as much. Also because of the reduced weight you're not experiencing the piston throw its weight to the top or bottom of the cylinder as much (dont mock, even at 70g a 66cc piston can throw 180lbs of force straight up or down). It'll never be perfectly smooth, sadly, but you can make it smooth for a particular area of speed.
I thought I deburred the ports enough but I suppose not. As far as pictures go, it was the first thing I did

I pulled off the body right there on the side of the road.
I will post as soon as I can get them on my computer.
If running at higher RPM's you have to not only deburr as mentioned, you have to chamfer (bevel) and round your ports as well. If you made them wider and squarer, then you're gunna have a bad time. If you Dont bevel and want high RPM, you're gunna have a bad time. Jag says rounding your ports makes more low end power but I see nothing about this in Jenning's tuner handbook. What you want to do is Make your ports wider, where you want them to be from the middles of the ports (that is the middle of the Y axis). Then curve from there down to the original port ceiling and floor. You may end up with a squished hexagon shaped port but it should work. Then, from the inside of the cylinder come from up top or underneath with your dremel and put a small bevel all along the top and bottom edges of the port. It doesn't have to be big, maybe a 10 degree cut 0.8mm into the port mouth. This wont change port timing much. Do the same to your intake port, bevel the upper and lower edges of the port mouth. We're trying to re-seat the ring as gently as possible without changing timing or knocking the ring out and breaking it.