Out of curiosity, how would the bolt hole(s) for the thrust main be modified to account for the front to back deviation and still allow it to fulfill its intended purpose?
Regarding #3 thrust, it appears that either the cap is drilled off center or the block saddle is. I'm guessing the cap is. The below will need to be done on a milling machine.
Measure the cap first, using calipers, measure the thickness of the bolt hole, to the side of the cap. If both sides are within .005 - .007, then it's good. Then do the same to the block bolt holes.
To fix the cap, put it in a precision vise, indicate across the bottom, to insure it's parallel and indicate the center of one bolt hole, on the X axis. After that, indicate the center of the of the cap, on the Y axis and "0" it. You will be at the center of the cap and where the center of one bolt should be.
Using a sharp, long 1/2" end mill (make sure it can go all the way threw, w/o hitting the vise bottom) and plunge threw the cap hole. Move over to the other hole, 3.680" and do the same. To insure that there is bolt clearance move .010 more in the Y axis and plunge again.
If the main saddle is off center, then you have to disregard the Y axis above and match the offset of those bolt holes, by measuring the offset and matching that on the Y axis.
Also, the circular cuts on both saddle and cap, are very close tolerance. The dimension is .913 - .915 so, check that also.