The miss can be from running rich. Even if the plugs are good, on a 2-stroke, it needs a good load to clear out sometimes.
Just a thought... make sure your high speed needles are closed. (toward the top of the carb, on the opposite side of the throttle cable) They have a little plastic cap on them so they are only 1/4 turn adjustable. I would pull that little cap off, and make sure they are closed.
As far as not running a cover on the PTO... it's really not a big deal, but you will wind up spraying a little oil and grease out, and it will get all over the engine compartment. OR... if anything breaks loose, it could fall into the moving parts. I have one sitting in the shop. PM me if you need it. (I'll sell it to you for $5 + ship)