If you need to purchase the flash components, I really like your first suggestion above. The Yongnuo YN560-TX with a couple of 560 III or IV is an extremely versatile arrangement. The ability to easily set manual power levels and trigger the flashes from the on-camera YN560-TX is extremely nice. (And you will only be using manual flash for image stacking). Between my son (also a photographer) and myself we've used a pretty fair amount of Yongnuo (flashes, transmitters and receivers) over the past few years. Initially I was leery of the reliability (based on web comments), but it has all worked well. (Naturally I can't guarantee what your experience would be
IMO your set-up (based on the picture you recently posted) really needs to be improved as far as maintaining a constant, rigid relationship of camera to subject (as long as there is nothing causing vibration in the scanner component). It seems this could be accomplished very inexpensively. Perhaps a solid piece of wood running under the scanner and extending enough to attach the camera to one end.
A Canon body like yours, with effective EFSC (be sure camera is set to use Silent Mode 1 or 2
when in live-view!) really will provide images with continuous light that are comparable to electronic flash provided there is no external, or "environmental" vibration source
. Perhaps I am spoiled since this is not an issue for me... as long as I pay close attention to some potential problems... no loud music, no washer/dryer running upstairs, no family members with "heavy feet" running around. I do realize that some people live in environments where it might not be possible to avoid all external vibration. Flash is then the best option. But I have moved from electronic flash to continuous light because it is so much easier to set up attractive lighting since you can actually see the lighting effect as you adjust the light positions.
Plant materials (especially cut sections) are extremely
hard to keep from moving or wilting during the acquisition of an image stack. If the entire piece in the picture moves "together" then turning on the x/y/and rotation settings in the stacking software will help immensely. But very commonly, parts of the plant specimen that are in the picture will move relative to other parts that are in the picture. This is a big problem, so mounting and bracing the subject carefully can help a great deal.