overall the changes look good.
make sure you default any new rules to how they were before you added the rule... aka EnforceSkillTimers to true.
interesting about the item bonuses being counted twice... have you checked #showbuffs to see how it compares?
also in the endurance calculation, what I put in should have matched your original version here:
http://www.eqemulator.net/forums/showthread.php?t=21661
I am assuming that the int() operators in your original code were being used in place of floor()... but in any light, the 0.075 * GetLevel() in your oringinal code was outside the int(), so it should have had the same rounding effects as my code. If you are really not intending to floor() those numbers, than instead of multiplying out each time like you did, just change the variables in that function to be floats and then use max_end += bonus_sum * GetLevel()*0.075; at the end. (converting an int to a float or vise versa is generally a rather computationally expensive operation, and should be minimized)