Hi. These are all good questions and you have a very interesting application.
The block stage should work well as a component of a probe station. The overall size is quite big, but the moving stage is in one corner, so four could surround a central probe area quite well. More than four would need more thought, but it would be easy to build a couple of stages and play with different arrangements. The range of motion is much less than the microscope stages, only about 2x2x2mm. If you just use the knobs to turn the actuators manually at first that gives a good feel for the motion that you can get. Motors add complexity, and they do move quite slowly, so doing it by hand is often good at first.
For a low magnification, there is a prototype Field Dissection Microscope that you could try, which is also discussed on the forum in First prototype of the Field Dissection Microscope is ready to build.
For x-y-z sample motion the Delta Stage is probably the best existing option. The range of travel is not as large as you would like - it is about 12x12mm. There is some discussion of modifying the stage in the thread “Substage for 2-photon microscopes”. That is about making the stage wider, which should be simply changing the parameter for the stage size, but caused some problems. For a larger range of motion you would want to increase the stage height, which may or may not work by simply changing the height parameter. This gives longer levers and more motion for the same maximum angle of the flexures (in x and y, but I think will not change the z range). It reduces the incremental motion and makes the stage less stable, so there is a limit to how far it would be sensible to go.
All of the microscope versions - the standard (inverted), the upright, or the delta stage can use reflection modules. There are not currently instructions for assembly of the reflection optics module in the standard microscope instructions. The correct STLs are available in the customisations and alternatives tab, but for assembly you would need to look at the Delta Stage instructions. Note that the optics modules for the Microscope and the Delta Stage are very similar, but the camera is rotated 45-degrees relative to each other, so you do need the modules from the right part of the project.
Overall you have a good plan to assemble a standard microscope first, and I would suggest you do that with transmission illumination. This has seen the most development in both development of the hardware and the instructions, so should be the simplest way in. You can build it upright or inverted, and in either case you can use high resolution (with an objective lens) or low cost optics modules.
The build techniques and much of the non-printed hardware are the same for the Block Stage and the Delta Stage, but those two projects are in a much earlier stage of development so it can help to have some experience of the way Openflexure stages go together.