Hmm, unassembled? That's a new one on me...
Assuming it was just the top end, that shouldn't be a negative as long as the motor was protected from debris getting into the bottom end and you have the basic skills to assemble the top end... Most experienced builders pull the top end on a new motor anyway, for inspection and removal of debris that is all too often found in the head...
You probably got the top end assembled already, if not, it's pretty easy. Most important thing is you need to take note of the opening in the rings and the small pins in the piston slot where the ring openings go. If you compress the rings in the wrong position you will break them, we dont want that to happen cause you will be stuck waiting for parts...
Speaking of waiting for parts, the head studs (all the studs on the motor) are usually pretty weak and crappy, SickBikeParts.com sells nice stud kits for not too much money. IMHO its better to build your bike with solid studs rather than letting the weak ones break on you and then having to deal with that situation. There are a couple different size studs, so make sure you order the right ones for your motor if you decide to upgrade them...
I set my studs into the block with red loctite, then use blue loctite when I put the nuts on the head. Red is stronger than blue, so the head nuts should spin off before the studs spin out... That said, I probably wouldn't use red loctite on the factory studs, cause they are bound to break and I wouldn't want to have to extract them from the block with red loctite on them. I also use red loctite on the intake and exhaust studs when I install them in the jug, then blue on the nuts. (I would probably refrain from using the red loctite on factory studs here as well) The vibrations on these motors make everything come loose, unfortunately aluminum is weak and threads strip out easily, so you can only torque things down so much. The loctite helps keep everything tightened up and torqued down properly.
With the studs in place and everything nice and clean, assembling the top end is pretty simple. I put one e-clip in place on one side of the piston, you should see the slot where it fits, make sure it is seated properly, then slide the piston pin through the other side. Install the needle bearing in the crank arm and apply a couple drops of 2-stroke oil to it, then put the piston over it and push the pin through till it hits the installed e-clip. The arrow on the piston should be pointing in the direction of flow in the engine, that is, from the intake pointing toward the exhaust. Now install the second e-clip, which is probably the toughest part....
When installing the jug I first lube the piston, rings and jug wall a bit with some 2-stroke oil to make things easier, then aligned the rings so they mate with the pins in their respective slots. I apply a thin layer of gasket sealer on both sides of the gaskets then slide the jug down to the piston. Compressing the top ring with my fingers I was able to get the first ring into the jug, slide it down to the second ring and do the same, it went pretty easy for me. Then work the piston up the cylinder a bit so the rings don't slip back out and carefully work the jug down into place.
Now you've gotta install the head gasket (I use a thin layer of gasket sealer on both sides) and then the head, and then torque the whole thing in place. The whole process kinda needs to be done in one shot without too much delay, cause you need to torque that head in place before the gasket sealer starts to set.
You can skip all the finer points if you like, like better studs, using loctite, gasket sealer etc, and just throw the jug on there and torque away, but chances are you will be revisiting it down the road, or at least having to torque again, and agian... but if you do go through all off the trouble to do it right she should hold pretty solid and not develop air leaks etc on you down the road....