EF 100mm F/2.8 Macro USM. Understanding that one of the primary differences between the "L" & non-L version is the Hybrid IS and that I use a tripod and light boxes - do you feel that the "L" version will produce noticeably higher quality photographs?
The L version is /likely/ to be sharper, but not by much. The difference is insignificant. Given your intended use it's an absolute non-issue.
would the additional range in F-stop be visually significant enough to entice me/you or would I have to make the jump to the F/1.2 to really get that benefit?
If you're often shooting wide open then you'll likely find a larger aperture lens more useful. The f1.4 and f1.2 are a lot nicer to use than the f1.8, mainly because of proper focusing rings. If going to full frame you'll get thinner depth of field equivalent to about one stop so I'd take this into account when considering an upgrade.
I was considering the EF 28-135 F/3.5-5.6 to cover a greater range for my walk-about lens - however I am open to suggestions.
I own the Tamron 28-75 f2.8. 28mm is not wide enough on a crop (though 50 or 55mm is also too short). Your problem of being focal length limited will get worse when you go full frame - that 28-135 you're considering will now be nice and wide but feel a little short. If you put a high value on quality my advice is to put up with lens swapping and either get closer or get the subjects to come closer. I know this sounds flippant but it really is good advice! Use bait and perhaps a hide. Develop a relationship with those squirrels so that they come to you.
Also, consider having the telephoto lens on as the default. Typically anything needing wider angles will be around long enough for you to change lenses etc.
Having advised against taking long range pot-shots at targets a lens worthy of consideration is the Sigma 50-500 OS. Not wide enough for many purposes but that 500mm gets you real close, whilst 50mm is still a very handy starting focal length for a lens. I'd rate image quality as okay-to-good rather than excellent, but it's a lens I'd love to own.