First of all, all the 3000 boxes were rebuilt by the D&RGW. They were essentially all new wood and the old hardware used on the "new" wood cars .... that's how extensive the rebuilds were. For tax reasons, they did not call them new. Since they used the old hardware, they qualify as "rebuilt".
The queen beams are 5' 9" on center for most of the cars ..... by actual measurement by Dave Grandt and myself on a trip in 1965 (or 67). Some cars varied an inch or so but not that much. I've always wondered where RailLine got the position on their boxes. Too close. The queen beams are just to the outside of the edge of the door.
OK. the beams are 5foot 9inch and the brake cylinder is right at 4foot 6inch. That leaves (minus 4 inch beam thickness) 9 inch clearance at the end of the cylinder for the pipe to turn and go hook to the train line.
On a RailLine kit, just move the queen beams to outside directly below each edge of the door above and you'll have the correct spacing with the space to put everything.
Remember that the push rod and clevis are through the one queen beam so the plunger end of the cylinder is right up against the beam (or very very close).
Look at the pictures and you'll see the space and positioning.
Remember that the strength of the truss rods and queen beams is best if they are positioned either side of the door opening since that's where the car is weakest but not under the actual door opening. That would be weak. The door opening posts sit on top (directly above) the queen beams.