might seem silly but check your plug wires. I have had wires with bad connections vibrate loose/together depending on forces...sometimes it would arc, othertimes it wouldnt. They were in the thick rubber area too, so they didnt visually look broken.

S13's are also notorious for timing chain rattle, it could be what is "knocking" but that is why its called rattle, a knock would be much more obvious...and its silly to say that rod knock is not a common occurance

Nissan MAF's go bad pretty often aswell. The whole intake system can cause some idle headaches....

Cleaning your MAF sensor with some electrical parts cleaner can help you a bit, and checking your intake system for air leaks is a good idea. A leak in your intake will cause a rough idle, and RPM's to drop when coming off of idle.