Ok, still trying to be helpful hopefully
Tom has given the dimensions for the ports, the slide valve and the valve travel and we've filled in the missing dimensions? We've deduced that the lap is 0.125" and the 0.5" valve travel should match the travel required in full gear. The size of the exhaust cavity is dubious and I think too big but that won't affect the setting of the valve.
What hasn't been mentioned so far is the peculiarity of Stephenson's valve gear in that the amount of lead it gives varies with the cut off/position of the reverser (Johnson bar as you call it). Stephensons is what is known as a variable lead valve gear as opposed to Walschaert's which is constant lead (lead being the amount that the valve port is open when the piston is at top and bottom dead centres. Lead can be positive and negative. If negative the port opens after top or bottom dead centres)
With the normal locomotive type of Stephensons the lead increases as the cut off is reduced (Johnson bar moved from full gear towards mid gear) and this increase in lead can cause serious problems if it becomes excessive. The amount of increase depends on the design of the valve gear e.g. the length of the eccentric rods etc. To stop this it is usual to design the gear to give zero lead (or only a small amount) in full gear or even negative lead in full gear. Many Great Western locos were designed with negative lead in full gear so that the lead didn't become excessive at the normal cut offs used for running.
This may be Tom's problem and why he cannot get the correct port opening on the rear port when he sets the valve for the front port. Tom's using a figure of 0.015" as the lead in full gear and it probably shouldn't be anything like this. It may well be a negative figure in which case the ports won't open until after top and bottom dead centres (Without the drawings of the valve gear we can only guess though) Basically, the valve won't be centred about the mid point of the valve travel using that amount of lead and you will get different port openings.
So I would suggest trying to set the valves with the Johnson bar halfway between full gear and mid gear and see what happens then. At that position the valve should have some lead at both ends of the cylinder and you should be able to centre it. Note though that the valve gear travel will be reduced and you will only get the ports opening say halfway.
Hope that helps and has not further clouded the issue.
John