Setting up a spare lifter to be for measuring pushrods & piston to valve clearance.

I have pulled the piston to take out the spring & replaced with just enough washers to get the clip in.

The small "disc", in the center of the piston, that slides in & the pushrod tip rides in, I have raised up to the clip as well, is this correct or should it be compressed into the piston?

Correct, You want it all locked solid which you have done. Going a bit further I stack washers so the cup is the same distance below the clip as the preload that I have measured from prior mockup checks as opposed to just being solid up against the clip. Might just be my OCD but this duplicates exactly what I have in my particular engine & I believe is important especially in SB's with the exaggerated pushrod angle. I would do 2 junk lifters so you can do intake/exhaust with the light springs.

If the purpose of this excersize is to check valve to piston clearance, the height of the pushrod cup in the lifter isn't critical, as long as it's basically solid.

To determine pushrod length, I would just pump one of the lifters up with oil and use that with the checking pushrod, cam on base circle, adjust length to just zero out the clearance.
Measure the length of the checking pushrod, add to that dimension the amount of lifter preload you want.......... then order that total length.

If you are using the stock nonadjustable valve train, shim so that the preload is in the lifter. If you are using an adjustable valvetrain, I'd do the same thing but make sure the rocker adjustment is at the nominal position when you measure the pushrod length.