I would be tempted to weld steel plate under there if possible, they're stuck there in a vulnerable spot for a tree stump. as long as it wouldn't inhibit proper suspension travel.
sometimes it can take time for the rings to properly seat... I remember when i rebuilt my mule, it would blow a small amount of smoke on start up, but went away within a few hours and doesn't use a drop now.
Did you have to Hone the cylinder, or have a machine shop bore it out?
Could also be valve seals leaking.