I have now finally upgraded my install to High Sierra. I learnt a lot, here are some notes that could maybe help someone.
How to make clone bootable backup, and I tested my clone before upgrading, in the end what worked for me was:
1) Use DiskUtility to create an EFI partition (tho I couldnt create it less than 5G!) and MAC on 2nd drive
2) Copy EFI bits from MACOS disk to Backup EFI partition
3) SuperDuper (free) to copy my OS partition
I could not upgrade without APFS, manually gave a 'licence agreement' not found. So I ended up going the default route with APFS upgraded. Now that I think about it, maybe I should have upgraded my clone (as it is non-SSD), and copy it back?!
Anyways, thanks all.