When I ask a question on here I expect real info!!!
Then may I ask why you expect something of people you do not know? We are here simply because we like talking bikes to one another and information we give out is purely at our own digression.
Lets break down what you've told us so far. In this one thread, you've said you blew up your engine, then the only information you've given us is that it is now back together and not running properly below 3,000rpm, then you asked why that is?
My first impression was that the bike is probably knocking because I had no idea you replaced anything beyond the rod bearings (and from the way you were talking to us, I had no reason to assume anything else). I called you a troll or said you were 'trolling the forums,' because I can't imagine any sane person destroying an engine to this magnitude and only putting bearings in, then managing to get it put back together enough to get it running, as it takes at least some technical ability and knowledge.
Now that we have established the following:
1. You replaced the internals that were possibly damaged.
2. If you had the block spec'ed out you are probably fine in that area, same if you had the internals measured for clearance.
3. The engine is back together, I assume now that it is not a knocking noise.
That being said, you still haven't given us any ideas of what it could be. You said it runs bad. Have you checked if all cylinders are firing at low RPM? Have you checked if they are all firing above 3,000 RPM where you say it clears up? It could be a magnitude of things that frankly, I could go down a large list step by step to check for every one or that you could give me a little information and we could probably get this handled online.
Last thing, this is all how trouble shooting works, I expect you are mostly new to this and would hope that you keep it in mind in the future when you ask a forum, or anybody else for help. I apologize for saying you were trolling, however given your attitude towards me, mostly that you expect help and that you are not grateful for it, that I will refrain from further help in this situation. Now if you are willing to apologize and I see that you understand that I don't actually owe you a thing, none of us do, I may come back to offer my advice (as I have a few ideas of what the issue may be already).