There's a hint here.
There are limits on how much current each 8-bit port on the 2560 is rated to provide to the corresponding output pins as well as a sensible limit of much less than 40 mA per individual pin. You really should not be expecting to provide significant current to multiple pins; that would indicate something wrong with your overall concept.
So the total current the 2560 drives to outputs is already limited to less than 500 mA. What you do not do is to expect to provide current to the USB port and expect to draw current from the "5V" pin; that is only marginally more practical than attempting to power it via "Vin" or the "barrel jack" which you have apparently discovered is indeed a most terrible idea.
You have a 5 V power supply for your overall project. Connect it to the "5V" pin and everything else that require 5 V (and needless to say, connect all the grounds). Just disconnect the "5V" pin whenever you plug the USB into a PC for programming or monitoring. 