The phrase 'in the same plane' had me more confused than usual. Now I think you're talking about, say, the first and last main journals of a crankshaft, and you want assurance that their axes are concentric within some tolerance in some arbitrary plane of measurement. GD&T guys use 'extended tolerance zones' to specify stuff like that.
I'm sure it's possible to automate the process, and I'm sure it's been done. I'll conjecture a labor- intensive process that could be done with tools that I might be able to get.
Set up four sensitive dial indicators, one at each end of each journal. Using a degree wheel, spin the shaft slowly on whatever axis can be arranged; between centers, journals on v-blocks, whatever. Every few degrees, record the reading of each indicator. Complete one revolution.
In a CAD program, draw four perfect circles in 3D space at the locations on the crank axis where the indicator measurements were made. Rotate your coordinate system, and for each data record, draw a radial line away from the perfect circle corresponding to each indicator's reading in the appropriate direction.
Then fit four perfect circles to the ends of the radial lines you've drawn. Or draw polylines enclosing those line ends, close the polylines, and find the centroids. Now you've got two points in space that define the ends of each journal's axis. Draw a line between them, extend it to whatever measuring plane you'd like to use, and find the difference in the intersection points of the two lines with the measuring plane.
Of course, you can do the same thing with numbers in a spreadsheet, but I thought the graphical description might be more illuminative.
-Mike-