Hi Brian,
The machine is a very interesting design. The driven shaft has a slightly off-center section to provide the swing of the oscillating head ( which the chisel bolts to) So it works a bit like a crankshaft. where it gets more interesting is that the oscillating head has a center plug with an offset hole bored through it, that fits over the driven shaft and cam be locked to that shaft in various positions radially providing an infinitely variable throw ( within the range) So you can vary the length of the mortise by adjusting the shaft and oscillating head. Of course all of the parts add room for tolerance, so you will have to check that all the shafts and bores are snug. then you can get and accurate readout of cut in reference to the axis of rotation and to the table.
There are several things that you need to check;
1. is the chisel mount surface a perpendicular plane to the shaft axis of rotation.
2. Does it stay a perpendicular plane during a full rotation of the shaft. Does it change angle of elevation?
Once you have established these two points are running true, then you can reference it to the table,
Once you get it apart and make sure that things are not cracked and bent and worn you will know more and be confident on what the cause of any problems will be. then it is simple a process of checking and verifying each step.