I still run Flex occasionally, but not on any real 6809 system – those are long gone except for a 6809-based eprom programmer which could not run Flex anyway. I run Flex using a 6809 emulator that I wrote myself a very long time ago. There are few of those out there, which are a lot more impressive than mine, which makes no attempt to simulate fangled things like FDC controller chips. Originally I used one of the versions of Flex that I had, and just patched the binary code in a few places to get it to work in the new virtual world.
Later, after the Internet was invented (!), I located the Flex source code and what I use now was assembled from that – it identifies itself as "6809 FLEX V3.01". It’s been a while since I set that up, but I think the code was as is in flex_srces.dsk here:
http://www.swtpcemu.com/swtpc/fufu_downloads.htm .
I made a lot of changes to TERMIO.TXT. For the strange way I do things, the FLEX FMS routines don’t actually get used, although I left that code there (long story, my emulator / virtual 6809 does not use .dsk files, at least not directly).
Just to get Flex to boot should not be too difficult if you set it up to do serial “terminal” access. If you already have Assist-09 running, you could just use that to load or even just manually enter the boot code for a test. A bit more work would be required to get the output to the CRT controller though. Keyboard, well, depending on what sort of keyboard you intend to use.