What was the engine rebored to? Was it checked for bore ovality and any deviation from vertical?
It may appear that there's a lot of clearance between the piston Crown and the bore when cold and I wouldn't at all be concerned about that.
It may well need a fresh hone and new rings.
How much Oil is it burning?
so the running clearance of 0.0025" stated for this piston is in hot conditions? http://www.minispare...-STN100-20.aspx
it uses about half a litre every 400 miles.
I must say I expected the new pistons and rebore to last about 3-4 times what it has currently done before starting to use oil at this rate.
How was the engine initially set up(fuel and timing?)
Half litre to 400 miles is excessive imo, however you say there was also a driveshaft seal leaking, are there any others?
it was rebored to 998 +20 and it was done by a machine shop I have used many times before and I expect they did what was needed, but don't know.
After the rebuild it was setup on a rolling road.
to my knowledge no other seals are leaking no so it probably isn't leaking that amount from a driveshaft seal, besides it still smokes on a cold startup.