Hi Stuart,
Great to read about your Applix 1616 restoration… certainly brings back lots of fond memories.
I have three 1616s which I’ll get around to restoring at some point.
The first one is my original personal 1616 which is the first prototype PCB we got back. It pretty well worked except for compatibility issues with some keyboards and VIAs, hence the pull-ups on the 6522.
The second one was used by ANSTO and was given to me as a gift by a friend of mine about 10 years ago.
Both these are the original 8Mhz 68k with the Z80 disk controller.
The last one was given to me a couple of years ago and is pretty well the same as the one you are restoring.
Glad to see the PAL’s you have are readable and can be copied. Unfortunately I don’t have the master PALs so was a little worried about this. All the early PALs were not copiable, as we didn’t want our masterpiece ripped off lol.
Anyways, super excited to see your progress
Have fun 
Paul Berger