Rich;
I don’t believe anyone has taken on the task of mapping the additional 16 digital pins into the Arduino IDE core library. It would be really cool if you can, I know the task is a little more software intensive then I felt I could handle when I looked at those library files after first getting my Seeeduino Mega. I’m more comfortable with the hardware side of these things. I did review your posted lists and I do think you correctly listed the correct ports and their bit positions for the additional 16 pins.
I think a few of the extra pins do have timers associated with them, but it’s probably something you would have to research better with the AVR 1280 datasheet: atmel.com/dyn/resources/prod … oc2549.pdf
So while I’m not up to the task of writing the code, I would be more then happy to test any changed IDE core files you want and report back.
I thought about this issues back whenever, and decided that if I really ever needed to access these extra pins I could write simple functions that would utilize the direct port statements to get to them.
Last point would be don’t be too disappointed that if you get it all working that the ‘official’ Arduino core team does not see fit to include it into an official IDE release, they may feel it’s a too vendor specific change 
Lefty