Glad to hear u have largely sorted the knee... Outside knee pain is quite often from an ITB cause, especially if you have just changed setups... Cleat angles and saddle too high are common causes.. Lots of other causes however of lateral knee pain, just identifying one of the most common...
But head off to a good orthopedic skilled doc or physio for assessment...
Edit: Whoops... Just read the last post about the right knee a bit more indepth... If its a loud audible cracking sound then this usually comes from tracking between the knee cap and underlying bony surface... Usually not much to worry about but can be a sign of some malalignment in ur kneecap tracking... Bit of physio and assessment of bike position etc should fix it...
