During the initial p0300 occurence, you may have been sending un-burned fuel into the cats due to the random misfire. This could have slowly started to clog the cats. Since you changed the entire coil pack, all spark plugs, cleaned the MAF sensors, and checked for vacuum leaks, this may have eliminated the initial root cause, but the secondary symptom has not yet been resolved. With the lower than normal flow out of the cats, this may be causing another random misfire.
This is all just a guess.. Let me know your results though. I had this code thrown without any symptoms. I did the same procedure as you and the code went away for several months, but it has returned without any symptoms again. Could possibly be my car is experiencing the same issues.
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