A. If I try to immo defeat the already tuned ECU are there any chances I can screw something up. Also I'm curious if I send it off somewhere could THEY screw it up.
Always a chance, but doubtful, as long as you have a backup of your eeprom and flash and known good boot mode setup
B. I have an automatic and the ECU is for manual. Can I copy the map file to my ecu and it just work?
Generally yes, but the EEPROM will need recoding (engine recode)
C. What's stopping someone from taking and tuned ecu and putting it into boot mode and copying the tune for a friend or whoever/making a backup of the ECU for yourself? Are there security measures setup to stop people from doing that?
Nothing, even if there is a riser.
Yes, there are methods, but not worth discussing here or anywhere else. Anybody set on "protecting" their OMG so great ME7.1.x tune is flat out delusional