Hi Nate,
I gave you a set of clip ons with the bike, didn't I? I think they were in the bottom of that spare parts box. I hope you didn't buy a set. BTW, if you put clips on it, you will have to modify the headlight brackets. There are a few posts on this board describing the procedure.
Anyway, the triple is a "your a peein" model meant for clip ons, not a machined US model. The two holes are for an extra bolt used on factory clip ons to make sure they don't slip. I dusted off the top with an end mill because the original finish was a little scuffed up from a key ring and the clear coat had come off in spots. The shiny spot is where I had my stopwatch ty wrapped on.
Later, Russ