Not familiar with that book, but I'd recommend laying off of the aggravating activity while on the anti-inflammatory dose. The effective anti-inflammatory dose of ibuprofen is about 800 mg, which is generally ok to do, but only for a short time (definitely under a week). I'm not saying you should start eating ibuprofen; I'm just saying that that's about what's typically prescribed for inflammation.
Taking a lesser dose and continuing to ride just masks the underlying problem while you do more damage. Better to heal up and figure out what's wrong. Taking NSAIDs long-term probably isn't a good idea, and definitely shouldn't done at an anti-inflammatory dose.
Of course, if you know you have knee arthritis, for example, and taking a small dose lets you continue being active, that may be another question. I'd probably see what drug the doc would give me, and let him do the deciding, though.
BTW, I always hated those commercials for aspirin or ibuprofen or whatever, which showed a middle-aged guy running and having pain. The message of the commercial was basically "pain during exercise? take drugs and keep going!" Seriously! Pain = something is wrong. If you don't know what's wrong, find out and fix it. if you know something is wrong, but can't/won't fix it, stop freaking running on it! I personally try to steer my clients away from distance running, generally. The exception would be if they are experienced and have no known joint/gait problems. Middle-aged joints, a couple dozen extra pounds, and poor gait mechanics all add up to injury when someone decides to suddenly get off the couch and start running. But now I'm getting off-topic...