Greg,
The original coupler height for the E&P was 24 inches. That is pretty low. Later coupler heights were several inches higher. The flat car and the combine I have made both have coupler heights of 24 inches and the draft gear on both is not end sill mounted, but rather mounted underneath as you described. Also, both have springs on the inside end of the draft gear. If you look at early pictures of the Billmeyer & Smalls passenger car "Eureka"s you can see the original setting of the gear. However in later pictures, and on the Palisade car at the NSRM in BC, the E&P (EN) installed a spacer on the car bolsters to get the height of the car raised to match higher coupler heights in later years. Since I was building the flat car and combine to the earlier period, I stuck with the original heights.
On my locomotive Eureka, the coupler pocket on the tender is set such that I can accommodate both the original height and the later height. On the Durango & Silverton the coupler heights are above 24 inches so I needed to be able to match their cars. Even then I found that their car heights varied somewhat, so I need to use an extended knuckle to operate safely with their knuckles. It is a world of compromises.
Dan Markoff