to the OP, first I feel your pain. I have arthritis in my neck that has crippled my left arm/hand. Can't handhold a 100-400 IS at all, hard to carry around a tripod. Have been using a monopod for years w/my 1.6 AP-C cameras.
I use the Carbon Fiber Manfrotto 694 w/the tilt head. Mount the lens shoe on the QR plate. Rarely even use the tilt feature and I rotate the lens w/in the collar for vertical. But the head has the QR for easy removal.
I try to hold my arms close to my body as I do w/just a camera, and keep them there as I tilt or rotate the whole assembly. Always use the vertical grip on the EOS to keep from needing to hook the elbow over the camera.
Keep IS on in all directions w/the monopod except for birds in flight..
Everything is a trade off. So I may have to use a higher ISO, like 800-1000 to get a sufficient shutter speed. Am hoping like others for a newer 100-400 IS w/better Stablization. I hate the push pull because the motion to extend the lens is literally a pain in the neck.