Knee Pain after cycling training

Just above your knee is the quadricep muscle/tendon junction. it sounds like you are putting too much emphasis on the downstroke of your pedalling as this recruits the quads. Check your seat position and maybe put it a little higher. Either that or get some deep tissue massage... hurts but its good.

Hey, what about your crank length (range of motion)? In my case I changed my old 170mm by a new 180mm (I have 84cm inseam), no more pain in my knee, so good feeling specially in climbs.
Other point, why not consider a short to long training approximation? and a strength conditioning program before? long mileage as alone basis would weak your tissues!. Which are your needs to work on?

An article on this website refers to excessive long mileage in amateur cycling. Most cycling programmes are general, but not personalized!. If you are heavy and have big muscles, long mileage will be good but also calls for knee strength workouts(as Armstrong in oct-nov preparing the next tour). If you are thin and have weak muscles and knee, lower mileage and other focus (strength) will be better.
Perhaps the repetitive dead spot at the final of your downstroke is bad for your knee, so you would need to liberate the force/weight on the pedal before this point. Also a Q-ring would help with this.
Check this article about rounded stroke (for your hamstrings), perhaps it would help:
http://www.posetech.com/training/archives/000598.html

General fitness is not only resistance, also strength. Let your knee and tissues to recover/assimilate each workout (approx 36h of rest as a PP article shows). Ask your coach "why a general workout" considering your weak links.

The more general program is simply to build basic conditioning, work on pedaling technique, increase overall cycling efficiency, and to improve the bodies ability to burn fat as a fuel source. With my lack of conditioning, to move onto heavier resistance training at this point would most likely lead to injuries and the basic conditioning is lacking.

With an adequate basic training, then I will move to what I call base 1 training, which increases time/distance to about 85% of maximum race distance, but introduces more hills, to add a degree of resistance to the training in a progressive manner. This phase will last from 4 to 8 weeks. After that, Base 2 beings, with less foucs on the "long slow distance" and more on muscular endurance, where periods of training with increased gearing to add resistance are incorporated.

Thie idea is the the training is progressively building the foundations, to allow the body to tolerate the higher intensity work to come after.

...I think you must check that your knee are at 90° when you start putting load at any point on the pedal downstroke, otherwise there would be a bad load on your knee tissues.
Perhaps a gently pedaling in reverse at the final of your workout helps to correct any acquired tissue unbalances.

You do not need good technique to pedal at high cadence, check what this PP article show:
http://www.sportsinjurybulletin.com/archive/lance-armstrong.html

"Training at higher cadences also improves pedalling efficiency. When you pedal faster, any inefficiencies in your pedal technique are exaggerated, so the correction of these and maintenance of good form at higher cadences ensures consistent efficiency."

"He complements this base training with strength work. The energy demands of endurance cycling inevitably result in lost muscle mass, which the strength training restores. But you have to get it just right: excessive weight gain through strength training can put a cyclist at a disadvantage. Armstrong, for instance, is said to enjoy a 10kg weight advantage over his fierce rival Jan Ullrich for the same power output, which helps him dominate in the mountain stages. (No wonder, then, that Armstrong is so meticulous with his diet – even weighing the exact amount of food that he needs to refuel his body after training.) Strength improvements result less from hypertrophy than from neuromuscular conditioning."

Also, I read in other PP article:

"It should be noted that your cardiovascular training will adversely affect your strength training but strength training will not damage your cardio endeavours."

So do strength for your knee!! You won't lose your training stage at all.

You are OK, no gain in performance, instead maintaining it without injury risk (at least)! Gains in cycling performance are so riding specific (but you can also do Inspiratory Muscle Training for your VO2 - check PowerBreathe).

You can do specific strength in climbs. Regarding no-riding specific strength, I think plyometrics are the best, we do them as regular basis during all the triathlon season (well, not at pre-competitive or competitive weeks), and mixed with weight lifting for general conditioning during the early season.

I think cycling is difficult to understand, so the best way is your own feeling. In my case, I am progressing with basis on errors!, most of them are bike fitting.