to answer my own question:
Ok, the source for boot1f32 had the key, but not the lock to put it into..... a comment with a dd command.
It's the correct command to copy the BPB (and/or the rest of the critical bits) from your partition to the boot1f32 file.
However, when I tried to run it directly on the drive (in osx) it complained that it was an invalid argument. I've just tried running it on a bootsector image that's saved to file first, and it worked! This is possible the long way around, but it has worked, and I'll optimize it a bit later one if I find time.
So without further ado...
[HOWTO] Install Chameleon onto FAT32 Drive
This has only been tested on Linux so far, but it should work from osx too. This requires some basic command line knowledge on how to navigate, find the relevant files etc.
1 ) Format the relevant partition (I used MBR partitions, which then has to be a primary one) as fat32 (or msdos from Disk utility).
2 ) find the correct dev for the partition - replace sda / sda1 with your correct drive path in all further steps!!
Linux: /dev/sda1 or similar
OSX: /dev/rdisk0s1 or similar
3 ) Get a command line / Terminal and type:
sudo dd if=/dev/sda1 of=blank_part.bin bs=512 count=1
now you've got a copy of the blank partition header.
4 ) Find boot1f32 and make a copy of it
sudo cp boot1f32 boot1f32.local
5 ) Update your copy to include the relevant partition information
sudo dd if=blank_part.bin of=boot1f32.local skip=3 seek=3 bs=1 count=87 conv=notrunc
6 ) Now you've got a boot1f32 that's customized to your partition, write it onto it - get the drive path right!
dd if=boot1f32.local of=/dev/sda1 bs=512 count=1
7 ) And update the boot0 code the normal way... check the drive paths again to be sure!
for linux:
sudo dd if=boot0 of=/dev/sda bs=440 count=1
for mac:
sudo fdisk -f boot0 -u -y /dev/rdisk0
8 ) and copy the boot file (from chameleon) onto the partition (mount it first)
sudo cp boot /mnt/sda1
or...
sudo cp boot /Volumes/boot
or similar...
and copy any other relevant files / Extra folder and so on as per usual chameleon install
Cross fingers and Reboot!
Hope this helps someone else,
Andrew