Muscles strengthen faster than ligaments or tendons. In fact, long before you add any new muscle tissue you get stronger by virtue of better coordination (recruitment) of the fibers. This newfound strength adds to the forces the connective tissues have to deal with and can result in small tears and inflammation, which is likely the source of your pain. The best advise I have for you is to back off, at least in terms of power. Consider forcing yourself to ride at a much higher cadence than you have been using and even traveling at a reduced speed when you do ride.

Take some NSAIDs, use some ice/heat cycles, let it rest a bit and ride easy when you come back. Not only do these tissues take longer to strengthen than muscles do, they don't heal very well either (no circulation). You might consider having an experienced cyclist or a quality shop look at your fit on the bike as well. A good fit can help prevent some of these problems.

Once you are healed, bear in mind the 5% rule: Don't add more than 5% to your workouts per week. It sometimes seems like it will take forever to achieve some mileage goal when following it, but you are more likely to obtain your goals if you avoid injuries.