Indexing Bolt Hole Patterns

To do it manually, I would do a template with a cad program matching the shaft ends, length and hole locations etc, and print it out 1:1, tape or adhere it to the shaft so each end folds over the shaft ends. Then center punch the hole locations, then drill on a drill press or mill. I would think the locations would be fairly accurate this way especially considering the short length of the shaft.
 
It depends how you are creating the shaft. If you make it out of solid stock you just need to drill 4 very deep holes. Then turn down the middle to be the shaft and give you flanges on the end.

If you are using plate for the flanges and welding them onto stock to create the shaft between them. Start with square plates and put a hole in the center of each one big enough to fit the shaft into. Press fit them and then a little persuasion with a hammer will square up the ends. Weld your shaft in between and then you can use an edge finder to reach a starting point which you can replicate on the other end. Once the pattern is drilled on both ends, chuck it up and make the flanges round.

Plenty of ways to skin this cat. Some will be easier than others.
 
Start with the shaft with a keyway in it full length. Using round plate for the flanges, cut the center hole and a matching keyway. Drill the hole pattern in the flanges together using a short piece of shaft and keyway to keep them aligned. Then attach flanges by welding them to shaft.
 
It will be a while before I get to this but thanks everyone for the suggestions. I will revisit this thread in the near future.
 
Clamp your shaft in a v block. Now hold the v block. Do the math for the bolt pattern. X cosine of the angle times the radius. Y sine of the angle times the radius. From centre move over your radius. This becomes your first hole at 90 degrees. No math here just move over your radius. Next hole is 180 degrees and so on. Take care of your backlash and it is accurate. Don t remove shaft from v block and flip over clamp find centre and repeat. Four choices here for indexing with the four sides of the v block. Orientate the v block for proper indexing. If it is the same just keep the v block in the same position as the first side drilled.
 
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Make the shaft a little long and mill an indexing mark in both ends, in one setup. After locating the holes off the index marks, face the ends to length.
 
Redneck engineering at its' finest... Take a length of bed rail and scribe both ends. Then take a center finder and at each end mark the line from the longitudinal one. That gives you registration for two holes. The other two can be done with a dividers. Then swing the circle radius do get bolt circle diameter. Once this is done, use the power tool to drill the holes.
 
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