I'm going to guess you actually honed the cylinder. Maybe used a glaze braker or ridge reamer. Standard drill presses are not accurate enough for cylinder boring.
45-60 is a pretty broad sweep. My kart topped out at 45, and I had some pretty good hardware happening.
Anyways, maybe there was a communications failure (most likely) or your uncle misinformed you (possible) or has absolutely no idea what he's talking about (gonna hope for not likely, but basically your information is weak at best.
You see, when someone shows up outta nowhere making hp/torque/speed claims and has nothing to back it, it's a bad start. Especially when the person proves to be, ahh, misinformed. I've seen it go worse than this.
Truth is, if you were to say, "I did some tweaking on it and it feels faster", or, "the GPS says I picked up 5MPH" then that's at least honest an makes no refutable claims. Further to that, if you were to say, "I really have no idea what I'm doing here and need all the help I can get.", then I personally guarantee you'll get all sorts of help here!
Anyways, that said- Tell us about your kart! (What you do know, like make, model, engine size, features, etc)
Oh- regarding the clutch thing- If you find you need to mount it too far outboard for the engine's shaft, your better option may be to move your axle sprocket over a little. There really is not practical way to extend the PTO shaft.