2005 tacoma running rough

About 1 month ago my 05 tacoma (4dr, v6) started running rough. Has a more 'throaty' sound to it, runs a bit rougher and seems to have lost some power, AND shifts at odd times, i.e. shifts down when it shouldn't and doesn't always shift up when it should. BUT, about every 2 or 3 days it will run like a top,like brand new. A buddy of mine thought maybe the EGR valve is sticking, perhaps a sensor/chip issue. There has been NO check engine/maint rqrd light that has come on. I'm sure that when I take it in to the dealership this week it will be running perfectly that day so they won't be able to find anything...
Also, if no maint rqrd 'code' is available, can the diag machine at their shop still detect anything?

ok its a 2005. you should still have a warranty so..... take it to the dealer!!