Mega 2560 R3 "1.0 added SCL and SDA near to the AREF pin" - huh?

Projects Networking, Protocols, and Devices
3

Yes, SCL/SDA connected in parallel to the other SCL/SDA pins.

Don't know about non-functioning vs Duemilanove - more info needed.

2nd ICSP header is for re-programming the 16U2 chip.