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The face you have just cut goes down into the vice with the same datum face that you used before against the fixed jaw. I set my piece onto parallels and tap the material onto that until it just grips the parallels, that way I know that everything will be square and parallel. But if the jaw is square to the base of the vice you should be ok.
Oh! and a little message for Eddy, here is the first wart (or pimple), the block was a bit tight to get out of the rough cast material an is in fact 0.15mm (0.006") too short on the height, but as I said, don't worry, all I will do is take the same measurement off the top of the piston and all will be right with the world.
The way I see it now, is that when viewed from the output end (the end connected to the shaft), engine going in a clockwise direction, with the nearest piston in the fully upstroke position, the eccentric will be 90deg to the right, the rear piston is on its downstroke and its big end at 90deg to the right (the same position as the front eccentric) and its eccentric 90deg fwd of that at full bottom stroke, or should the rear piston be on its upstroke and it's eccentric be at the same position as the front pistons big end? Or doesn't it matter.