I would let it set in a warm, dry, sunny place for a few days and see if this fixes things. If it's mildew the sunshine might be the cure. Some urethane finishes can out gas and produce bubbles, but it's not likely unless the rod is very new.

You can use automobile polish/finish/cleaner to remove slight imperfections. These products are vey fine abrasives used to remove paint defects in auto body finishing.

This can be done with the guides in place using a lint free rag and plenty of elbow grease. I have used 'Mirror Glaze' Fine-Cut Cleaner #2 with success. There are many similar products avaialable, such as 'Finess-It' Check you local auto parts store.