Yes those AGA extra graphics eat the machine regards base 2MB chip as you say and with regards to using 2 disks to ship the end game on.
Anyway, I further tested Shrinkler with colour poke and text message options and will run with it for now. I can now fit the .exe on disk 1 at least without taking anything out of the game given everything is heavily compressed already pretty much.
For anybody remotely interested in this particular subject and Shrinkler, I used...
Code:
shrinkler --textfile decrunch.txt --flash DFF180 cp2 cp2.srk
Which ends up looking like this (sorry it's a bit large off the emulator screen)...
It'll do