Are you vent lines rerouted? You will probably need to drain the carb. Also if I were you I'd change the oil 3 or 4 times while riding the bike for about 10 minutes between oil changes.
**** you had a lot of water in it!!I changed the oil 9 times so far and guess what its still milky!!! Not to bad Maybe two more and it will be good but I got most of the bad stuff out and I am gunna crank her up tomorrow and cruise around the yard then change it again! But I almost got it done and it runs perfect!
I would not you might have mud in the oil too and if the filter was not in there the mud would not be stoped by anything.Couldn't you just leave the oil filter out while you're going through the sequence of changing the oil to get the water out?Then put a new filter in on the last time changing it?