Sal,
Futaba said the 40 55% thing should NOT be a visible difference.

I think I found something, Im not sure what to make of it but none the less my servos are tracking perfectly together right now .

Heres what I did,
1. Fully charged batteries.
2. Made a note of where I had my up and down endpoint values set on both elevators.
3. Set the all the endpoints back to zero on elevator channels 2 and 6.
4. Gave full "up" input on the stick and started increasing the endpoint on one of the elevator channels.
I eased it up until the servo reached the point where it started chattering and backed off 2 clicks. Then I did the same thing on the other elevator till they lined up, fortunately the 2nd elevator never chattered before they matched up.

Heres what I ended up with for ep settings before and after
Channel 2
Before
up 65 down 60
After 49 down 44
Channel 6
before
up 100 down 100(?? I Dont get this, why are the 2 channels so different??)
after
up 100 down 100.

So I raised the settings on channel 2 back to 65 and 60 and the whole problem came back and I didnt gain anymore throw.
Went back to the 49 44 setting and everything is perfect and I have about 43 degrees of throw. I dont think the numbers matter, what matters is not having your EP set beyond what the hinges or servo/ servo linkage can give you.

Here is what I think.
I had the endpoint setting set way past where the elevator could actually travel and so it was getting to the mechanical limit of the servo before it reached the computer endpoint, which was also screwing up the expo. This threw the timing of the 2 separate elevators off bigtime.
Now that the elevator is only being asked to travel within its mechanical limits the computer is able to synchronize the ep and expo so that both surfaces move together. At least its working for me.

If you are having this problem try this, it worked for me.
First, if your centering is off, fix the linkage or subtrim to get the surfaces both neutral with the transmitter and receiver on.
1. Switch to high rate
2. Go to the EP function, Set your elevator EPs on zero, all 4 of them (2 on each side).
3. Pick elevator channel 2 or 6 give full up/down,, nothing should happen( zero endpoint)
4. start increasing the ep till the surface gets to the desired angle or mechanical limit. If you hit the mech limit back off a couple of clicks.
5. Go to the other channel and do the same thing. If the mechanical throw limit is less than the other channel then you will have to back off to satisfy the lesser mech throw limit of the 2 channels.
6. Do the same thing with down elevator.

I may be nuts, let me know what you think. Its working though,, go figure.