Stefan, judging by the number of motorcycle rental and tour companies operating in CR, this is a popular activity. Anything that's popular usually indicates it's pretty safe (people have a great trouble aversion gene!).
Here's our take on roads and road afety in CR
So apart from the potholes and dodgy roads, and the need to lock up your possessions securely at the end of each day's ride, it looks generally safe.... well, as safe as motorcycle riding can be.
As for best route, I'll ket others give their tips. But why not have a look at the routes the tour companies use, and maybe follow their example?
Good luck about 7 years ago
People drive horrible in Costa Rica so be careful :)
Pay for the data plan on your phone so you can get maps if you need them (if you have GPS). Other than the big main roads, signage is poor or nonexistent.
Potholes are awful! And many roads are dirt/dusty so be EXTRA prepared for this.
And everyone says DO NOT drive at night even in a car (unless it's a main highway) but more so if you're near pot holes and I mean pot holes 4 feet across :) about 7 years ago