If it's bad enough that you've got pieces of piston wedged in between the crank and case, or crank bearings that were seized, then that engine needs to be torn down and completely flushed out. If you are lucky, the crank is ok, and can be reused once it has been flushed to remove every last bit of piston that is stuck in it. If you don't get it completely cleaned out, the crank will not live long after the rebuild. It may still not last long depending upon how many chips went through the bearings.
Sorry to say, but your safest bet is to tear the engine right down, flush it out and go through everything. If you want to gamble, you could try flushing the crank without splitting the cases, but you may not get it all, which could toast your new top end in short order. For the slight added expense to tear it down completely, I wouldn't risk it by trying to avoid a complete disassembly and going over.