KZ 400 Bobber Project

So the other project I am kicking off this weekend is turing my 75 KZ400 into a bobber.  I replaced the battery and the plugs but the bike is running really, really rough.  It is getting gas, spark and the compression seems pretty good but there a a lot of variables to look into (ignition unit sending a weak spark?, bad gas?  blocked jets?) so the next step is to empty the fluids and start stripping it down to the frame and drag it into my little work space in the basement.  This is probably going to be the priority while I figure out exactly what I want to do with the Ducati project.