Yamaha 1300 Tourer - Yamaha 1300 Tourer Fansite

So I just did an oil change on my '09 1300, and even though its an '09 its new off the lot. Didn't even have 1 mile on the odometer. I used 20-50 Yahaha lube as recommended in the service manual. My wife thinks the bike is running rough after the oil change. I however think its running fine and that its just changing its tone during its break in period. I'd like some of you more experienced 1300 riders opinons on this.

P.S. the valves have been checked and are set correctly.