I've thought about installing a girdle on my industrial engine but, the girdle price ($450) stops me. I realize there isn't the same volume as SB's but, I always set limits on what I'll pay for something. So, I've thought about how I would install one.
I wasn't aware that the saddles were off that much. I didn't measure the saddle height when I had my Edsel on the mill. So, I think that I would start this, by paralleling the saddles at #1 & 5 and taking a clean up cut on the top of the china walls. That would give you the best average height to lean up the saddles.
I would diffidently use dowel pins in either 4 or 6 locations, inline with the center mains and I would use 3/8 Pull Dowels, to do that, they have a 10x32 thread so, you can take them back out. You would drill and ream the girdle 3/8, giving a .0002 press, in both the block and girdle, locating the girdle with 4 flathead bolts, to center it first.
Regarding making all the c'bores the same, I would install the caps and then run a 1" sq bar across them (shimming if necessary) to hold them in place, then c'bore. Then come back a ream 5/8" x .32 dp. Then use the below doweling.
Finally, before honing, I would use 5/8 hollow dowels, for each bolt, from the girdle, into the caps. Only going into the cap ~5/16". Since the spacer thickness would be fixed, the dowel section could be integral with the spacer. Of course the trust would have to be aligned first. The hollow dowels could be a press fit into the girdle. set the girdle on the caps, work it down, install the 3/8 dowels and torque. You could also use hollow dowels at the bottom but, you'd have to do that first, after surfacing the register area.