First of all, keep it simple. Could it be a fueling problem? Is there anything in the oil? Eliminate all the simple stuff first.
If it is engine problems, then is there excess vibration/noise? Where is this coming from? Topend? Bottom? Does the bike shift OK?
If it is a pre 04 R model then they are worth a lot more in parts, unless, maybe, you found the correct buyer and the bike was mint.
It pains me to say this, but if there are serious engine problems, then it is much cheaper/easier to drop a replacement engine in. The only exception to this is if you are experienced stripping engines and have fast access to used engine parts.
I replaced an engine when the valves and piston came into contact. One of the valves had snapped and ended up perpendicular to the piston, digging itself in by about 8mm. Its messy. It was uneconomical to repair. I still have the seized engine here, and there are loads of useful parts on it. Sprag, stator, starter, starter gears, gears, clutch plates, casings, good front cylinder head e.t.c. So you see, you can strip the old engine at your leisure and sell off the good bits.
What you really have to do is try all the easy possible solutions, before you buy a replacement engine. It is quite easy swapping engines, but as already said you should inspect the sprag work you have already done.