A few things to check and or change. Get rid of the Fox plug and install an OS 8 or a Sig GP-002 plug. Next check all the engine screws especially the rear cover ones. Next you mentioned that there were no leaks at the "O" ring under the carb that you installed. Did you maintain some downward pressure as you tightened the draw bar? Does the fuel you are using contain at least 18% oil of which at least some is castor oil especially during break in. Does your pitts style muffler have the pressure fitting in the correct place to provide correct pressure?
If it were my engine I would, at this point, put on the stock muffler and mount it to a stand to get it dialed in and broken in. If it wont run properly that way, it should go back for replacement or repair. You are introducing too many variables all at once with the cowl and with the non stock muffler and a new engine that hasn't been broken in or dialed in. If it runs fine on the stand the problems are with the exhaust and lack of cooling with the cowl.