What media card reader are you using? If it's one of the Mechware ones, I use them successfully in both my A500 (with external CD drive) and A2000 (with internal CD drive). You might want to check your termination jumper, otherwise you should have no problem running an internal CD. Using an external chassis to house the CD drive seems like a huge waste of space.
It shouldn't matter what your device ID is for booting, I boot from 0, or 1, or 5, or whatever. All that matters is that the devices are set to different ID's, terminated correctly, and show up as "bootable" when you open the Early Startup screen.
Also AFAIK most GVP accelerators map their memory into the 32-bit address space, so shouldn't conflict with the 16-bit address space limitations of the bridgeboard. Try running SysInfo, it should tell you if the memory is 32-bit or not.
Also, good luck with that Thylacine! It's a dog in my A2000, laggy and slow when it even detects a device at all (or doesn't freeze up), and this is with an '040. I've been meaning to try it with the original Thylacine software instead of Poseidon and see if that's any better, otherwise I'll be selling it on. Really seems to need A3000/A4000 ZIII bus.