You can go crazy, if you try and realign a set that was taken apart and put back together, "Just a tad off". Its one of the biggest reasons the muffler exhaust rubs the hole on the top and elongates it.
ALSO!!! if you see the hole elongated, check your vibration dampers. I saw one with a huge elongated hole in the top, as I was walking a motor line. Thats the only reason I stopped to look. The hole. Inside the set, three of the four vibration damper were broken. The engine and main gen had shifted to the side,main gen to the left, engine to the right. It wore a hole in the battery, the fan had tore the fan shroud up and the shorted battery had caused a fire. This gen set had just came back from down range. The Motor Sgt told me they could not get parts for it, so they ran it till it died.