"...I'm just getting back into photography after a couple of decades. I understand the issue and will have to either revert to the 100-400 for those fast action shots, or learn to manually focus (i.e. improve my skill). I guess that's part of the price you pay for getting a $2.3K setup versus a $12K (new 100-400 f2.8 lens) setup."
Um, I think you are refering to the new 200-400/4L IS 1.4X that lists for around $12K US. Heck of a lens, but it's not f2.8 and the focal length range is 200-400. And it has a built-in, carefully matched 1.4X teleconverter, so no need for one of those. With the 1.4X engaged, it's an effective 280-560mm f5.6 lens. Even at it's high price, IMO it's a bargain. I figure for most practical purposes it might replace around $20,000 to $40,000 worth of prime lenses (200, 300, 400 and 600mm), which would be impossible to carry around without a pack mule.
Your 100-400 might see more image quality loss than you like with a teleconverter on it... or you may be happy with it. You can get AF to at least try, though, by using the trick (already mentioned above) taping up a couple of the electronic contacts on the lens or teleconverter. Do a Google search, I'm sure you'll find some info online about how to tape up the contacts. It's an old trick that some people use to fool the camera into not recognizing that the teleconverter is there and still trying to AF. Depending upon the light conditions, subject detail/contrast, distances and other factors, the AF may work fine or might not work particularly well... In some more challenging conditions it is likelly to be slow or hunt or completely fail to achieve focus. OTOH, it's easy enough to try and might work for you.
I'm an old manual focus shooter from way back when, too. I resisted AF until I switched to Canon in 2001. Now that I've learned to use it well, I'll certainly never go back! AF is far faster and more accurate than I ever was, trying to focus manually (and I was pretty darned good). I'm not the only one, either. I've got an old Thomas Mangelsen print that dates back to his early days shooting with manual focus cameras, where it's obvious he wasn't any better than me manual focusing! I keep it framed on the wall to remind me that there's more to a fine, salable image than a lot of the bloggers today would have you think, reading all posts the obsessing about lens sharpness, focus testing and near impossible, pixel-level perfection they all seem to be seeking. 
