I tried to get my right-side CV shaft out to replace the inner boot, but it just didn't want to separate from the intermediate shaft (I didn't want that to come with it, so I left the bearing support in place). There didn't seem to be anywhere safe to pry, so I had to try hammering on a pry bar held up against the inner joint housing, but because I was lying down I couldn't get enough leverage.

Is there a trick to this, or a certain spot to use? I note that the Ford special tool is basically just a U-shaped piece of metal with a long handle, which you position behind the inner joint housing and pull.

Or should I have removed the bearing support and just popped out the whole assembly, including the intermediate shaft, and separated them off the vehicle? I'm guessing that it's safe to pry on the intermediate shaft where it enters the transaxle.

Something else that I was pondering over: Ford says to use a special tool to pull the CV shaft back through the hub when reinstalling. I got it as far in as I could, which was just far enough to thread on the old axle nut, and then I spun it on with my impact gun and pulled the shaft through. Worked like a charm - there's no reason why I *shouldn't* do that, is there, given that the old nut should be discarded anyway? It might as well do one final job before hitting the junk pile.

 

Don't bet the farm, but I think the center support has to come out to remove the shaft. The support and the intermediate joint have a bearing built in, the joint just allowing flex.
It should not be difficult to un-bolt the support bracket, let it hang, and yank out the whole assembly. There is just a small circular spring-wire that gets trapped in a slight groove retaining the shaft. It is not actually necessary for things to work, but the assembly line needs them, I think.
You do not want to disassemble the shaft pieces, inner from outer, while the center support is still bolted in place.

 

You definitely can remove the outer shaft while leaving the intermediate shaft in place. It's covered in the FSM, with an illustration of the special puller tool used to separate the outer shaft from the intermediate shaft - basically, as I mentioned before, a U-shaped piece of metal on a long handle that you slip behind the inner joint housing and use a bit like a slide hammer to bang on the housing with a pulling motion to force the shafts apart. You need to leave the bearing support bolted in when you do this, otherwise you'll pull the intermediate shaft out as well.

There's also at least one YT video of a guy knocking the outer shaft off while leaving the intermediate shaft bolted in, but it's clearly a crappy job if you're having to lie on the floor while you do it. Definitely easiest when the car's on a lift and you can be standing up and get a decent swing on the hammer. I gave up after about 20 fruitless minutes, as changing the boot wasn't an immediate priority.