The Jig plate needs to use the 1 1/4" and the 1" diameters on all parts as locators = one jig for the cylinder, pumps and that spacer, something like attached. Think a 1 1/4" counter bore with a suitable 1 1/4" to 1" reduction bush, then a pair to take the 1 1/4" counterbore to a 1/4" boss and 1 1/4" to 1" boss to register in the bores of the cylinder and pump.
Once you have started you need to leave the jig where it is for the second set of bores and do all three parts without moving the jig - I'd clamp some how not bolt it in place. If you look at my sketch you can see holes to hold the bushes in place and another set of holes round the outside which I would used for the clamp bolts.
Jo