From that statement, I'm assuming you're either replacing current one with new due to damage or wear, if so and again assuming obtained from a braker/stealer, have they sent you the right part?
If none of the above and you've just rebuilt the fork/s replacing bushes/seal etc, you must have left something out as they really only go together one way without extreme force of course!
New stanchions from ABE - and just the way that they do the bottom of the stanchion. Overall length of the stanchion is correct. All parts present and correct as per the fork inners picture posted above.
The think I cannot understand is the difference in lengths involved. For the damper/stanchion, it should be 755mm (ish) based on the length of the stanchion and the damper (taking the rebound spring into account)
The overall length of everything inside according to the Yamaha manual (measurements above) suggest there's a 40mm difference which is what I nearly have (25ish) but experience tells me that when everything is assembled the top of the spacer tube should be in contact with the cap when the leg is fully extended - not a 25-40mm gap.
Thinking about it logically, and having been out to the garage to measure it all up again, the stanchion is 595mm long. Allowing for the bottom part, lets say 590 of space to fill.
Allowing for the rebound spring (25mm) and the top of the damper (5mm) that leaves 560mm to be filled up by other bits of metal.
325 for the spring
200 for the spacer
1 for washer
10 for cap
=======
536 <-------the numbers just dont add up - Time for another coffee
It must be something like Unfazed has mentioned and a collar meant to be in the bottom of the stanchion that does not appear on any parts list (or evident in the ones I have binned now) that prevents the damper seal/spring from going to the very bottom of the stanchion.