Robin - the only lens I have with IS Mode 3 is my 100-400 Mk2 and it is a great advance on previous IS systems as it interferes much less with AF and tracking. This is great because this is the only IS lens that I have that I ever use IS on! I didn't realise that you had the 500 Mk2 - very nice!
According to the Canon Rep I referred to earlier he advised turning off IS at higher shutter speeds (1/500 sec +) as it serves no function. As he explained there is simply a limit to how fast the elements can respond/move! Apparently this is standard advice from Canon or so he tells me. Naturally if you have a perched subject in low light then things change! Just a personal opinion but I would suggest that you leave IS off and turn it on when needed? This will vary according to your abilities and which IS system you have (the latest in your case) and how your lens is supported - hand/tripod etc.
I am still intrigued to try a Gitzo Gimbal out - the fluid function might be advantageous in some circumstances, the price is sensible and it will match my tripod