The left pin in your first pictures is a tapered pin, with an adjustment knob on the top side of the plate to move it in and out. It is used to fine adjust the dimensional relationship of the tenon to the mortise, to get the desired perfect fit of the tenon to the mortise. An 1/8 of a turn of this knob will change the mortise and tenon fit by about 0.001". Once set, you can create mortises and tenons of the exact size relationship to fit together perfectly.
I have an early model FMT jig, but I have a knee problem that will keep me from getting to the jig to be able to measure it for a while, so I hope you can find someone else who can provide your needed measurements. They need to be quite accurate, not only for the pin spacing, but the pin to router bit center measurement as well. It would be best to make the plate from aluminum, since moisture changes in a wood plate might seriously affect the accuracy of the jig. The taper on the pin is going to be hard to measure too. It's this accuracy that is likely the reason why a replacement plate is so expensive.
How in the World did the seller manage to loose the top plate to his FMT? He likely still has it attached to one of his routers and it is some place in his shop. Maybe you could help him search for it (and maybe find some other goodies in the process). If not, deducting the cost of a new top plate should be part of the pricing for what is left.
Central North Carolina