+1 for the comments on a potential leaking header pipe, or general leaks anywhere.
Ive had exhaust off more than i care to mention so mostly when the bikes running bad its because the header bolts come loose, gaskets stuffed there, or the seal between pipe and muffler has loosened.
The header pipe into the head is a weird fit. i bought loads of the gaskets but also used gasket glue which works really well too. You can put your hand near the header when the bikes running and if you feel air pumping onto your hand, that seal isn't sealing.
Every now and then my pipe loosens somewhere causing leaks and i quickly fix it. first thing i notice is the bike sounds different, worse, and then performance. coughing spluttering etc.
closing the exhaust system up turns into Burt Munros Indian Scout.