The last time I did this--admittedly, years ago--I started by drilling the three screw holes for the boot flange. The screw holes were dimpled in the pan (on an original) so that was easy. I then started assembling the linkage starting at the transmission working back to the countershaft. I drillled the hole for the countershaft using the shaft's bracket as a guide. Once the boot was in place, I was able to completely assemble the linkage, locating the pivot bracket and shifter to it, both bolted to their floor brackets. At that point, two of the brackets pretty much located themselves and could be welded.
Once those were in place I screwed the rear bracket to the console, strategically slathered some paint on its tunnel contact points, and carefully set the console in place with the paint still wet 'n' sloppy, being careful to get the screw holes aligned. After lifting the console, I had a nice area of wet paint on the tunnel, the perimeter of which I marked before cleaning it up. I welded that bracket in and boom--as good as factory, maybe better.
It was
way easier than trying to be "exact" by screwing around with measurements. There is no "exact" on these cars. They were not precision-assembled by craftsmen. They were slapped together by guys with hangovers trying to get through the day while a shift foreman yelled about geting more cars built. For a more-accurate installation, peform the entire operation with a headache while your wife yells about the house needing paint and your mother-in-law reminds her she could've married that nice Jason Voorhees boy that took her to the prom.