Total aside, but I've been doing a LOT of lens testing lately and while some MF lenses like the Rollei Schneider ones reach their peak sharpness at or near wide open, many others such as older Zeiss MF are still developing sharpness stopped further and further down even as they become affected by diffraction. Like Bart suggests, knowing the behavior of your lens will help you decide what aperture to use. If you shoot at f/8 you'll need more frames for stacking.
But I am still wondering if you can't get a 'workable' image backed off a fair bit, not just a few inches but a few feet back. Your lichen sample may only fill but a fraction of the frame, but you may get the whole of it within DOF then in a single frame. I'm not sure what your intended use is, but perhaps if you end up with a3000 pixel wide crop with a sharp image it would be sufficient for your use?