You need to re-torque the head bolts. It's pretty much a "must do" on one of these when you get it. It's common for the bolts and nuts to loosen up because Yamaha used rubber washers under the 4 outside acorn nuts on top of the head. They're too soft and allow those 4 nuts to come loose all the time. If you don't keep after it and re-tighten them, a leaking head gasket is the result. Many of us replace those rubber washers with copper or brass washers. Those 4 outside studs flow oil, that's why Yamaha put the rubber washers on them. Brass or copper is soft enough to seal the oil in but hard enough to keep the nuts tight.
Yes, your side covers are from a Standard model, but your bike is definitely a Special. There are a couple differences and "tells" on the frame. The rear shocks lay down at a bit more of an angle and the bracket for the passenger peg and muffler hanger is just a curved tube. The Standard has more upright rear shocks and the muffler/passenger peg bracket is a loop.