What it sounds like to me is a serious case of "oops I didn't add enough oil to my dry sump engine" With a dry sump type engine, the oil has a very specific way it needs to be checked... but in short, the engine needs to be run for a couple of minutes to circulate the oil through the engine, then with the engine stopped for a bit, the oil level can be properly checked.
Did you happen to measure how much oil you used to re-fill the bike after you had it apart? I would think that you only got about a quart back in before it overflowed... (not enough...) The oil pump is behind the filter assembly, so chances are that you didn't do anything wrong when you had it apart. But, it does sound like you hurt the engine pretty bad. Sorry to hear about your troubles. Good luck with it!