Bootloader: the verification mismatch problem is solved, it was an avrdude bug. If you change the aduino avrdude to the last version you do not have this message.
Another important thing is that the error was only on verification, the bootloader normally work also whit the old version.
Programming: You use the Upload by programmers command under File tab ?
On the Uno after programming, and after a manual reset, the Blink work, on the Mega it is necessary change the RST Fuse. I do not know why this difference, I working on it for an exlanation.
I have a Guide, in italian, in my sign
So it is possible bootload and program via ISP the Mega 