I'm not sure that a blowing exhaust could give these symptoms - shuddering then being OK. Sure it could affect power but wouldn't go away, just get worse (and louder) over time.
You are probably experiencing a misfire. That opens up a whole host of possible causes relating to electrics, fuel or compression.
That's assuming it ain't when you change gear 'cos that would be a clutch judder problem. If the clutch was really bad I guess it could judder when extra power is called for (acceleration).
red