Is it possible to do some HW changes on board Arduino MEGA R3 for low power?
Is there any solution for it's disconnection from power source?I managed software well (deep_sleep), 
now I look a good solution for HW part...
This is a tutorial for the ATmega328P, the microcontroller that is used in the Arduino Uno : Gammon Forum : Electronics : Microprocessors : Power saving techniques for microprocessors
For the ATmega2560 it will be harder, that chip is not manufactured with PicoPower.
To make the Arduino Mega 2560 board use less current is not easy. You would have to remove the voltage regulator, and make a few other changes. Is there an other way for your project ? Do you really need the Mega board ? What event should wakeup the Arduino board ?
I use external interrupt (from RTC - SQW pin) for wake up. There is a lot of peripheral which I use...
The input current is 24 mA regurarly - I haven osciloscope and so I think it is smaller when sleeping. It wakes up per one second and serve some small rutine and go to sleep. I have an Idea of 10 mA.
Is there some jumper fo disconnecting the "second" procesor?
I save about 3 mA when I disconnect power LED...
Where I save about 10 mA? Any idea?
It is possible to set the ATmega16u2 in DFU mode, but I think that won't help a lot. I don't know if there is a sleep mode already programmed in it. I think it is not. Perhaps you can write your own code that puts the chip in sleep mode when DFU is selected. I have not done that, so I don't know how to do that.
If you make RN5C and RN5D 1M then the voltage switch might become unstable. When both are 47k it should still be okay.
What do you do to enter the sleep mode for the ATmega2560 ?
In SW I disconnect all unused peripherals. Software is very comprehensive and so I can not send it for inspection. I think the SW part is OK. I am looking guzzler (appliance) on the Arduino board. For example, featured a R divider (RN5C and RN5D) consumes(burn up) 0.25 mA. I think that there is some other appliance on board.