Hardwood floor finish / plugs?

I just finished installing a hardwood floor. It is a nice 5 inch purpleheart wood from Lumber Liquidators. However, since it was on clearance, there were defects in quite a few of the pieces. I'm trying to figure out what can be used as a patch on the finish, but I imagine that different products are going to come with different finishes. All I can say is that the finish isn't very strong or durable.

Also, we have quite a few screw holes to plug. We were thinking we would take some of the extras back to the shop, plane them down to something like 1/4 inch, and use a plug cutter with a drill press. Is there an easier way to do this? Is there a company that sells dowels in different hardwoods for this purpose? If we do that, we'll have to match the finish, of course, which goes back to my previous question.

Any help in this area would be appreciated.