On your Ultra, the oil pan is on the bottom of the transmission. If you pull the oil dipstick, you'll see that it goes down into the pan located under the transmission. The engine oil drain is the drain plug nearest the left front of the pan or in the middle of the pan. If the bike is on the side stand when your drain the oil, I'd pull the plug in the front so that all the oil comes out. If you pull the one in the middle, you must stand the bike up straight to get all the oil out. The transmission drain appears to be the pipe plug in the front of the oil pan. Go to www.bikebandit.com and pull up this drawing. It will show you the pan and the gasket. Notice the gasket closely, the hole down through the front of the pan looks like it goes to the transmission and the other plugs look like they are for engine oil. The plug you pulled out is the drain for the cam chest, I think. I'm not a Twin Cam mechanic but I'm pretty sure that I'm right about that particular plug. You probably didn't get any more than a couple of ounces of oil out of that area.
http://www.bikebandit.com/1999-harley-davidson-flhtcu-i/o/m1173#sch145241
Good luck
Steve
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