Terry,
I have done a few of these jack-shaft bearing replacements now, it's a horrible job. Like you suggest, I get rid of the silly 'cap-head' over stud arrangement and use conventional 5/16th UNC cap heads on all of them under the shaft. That way, you can remove them with the shaft in the casting. Whoever came up with that original design should be taken out back and shot. I do install all 3 bearings, not sure if it would 'whip' with only two? the center one has normally spun on the shaft, I have machined it down and installed a spacer (hot) and then machined it back to 25mm; this works provided it's not worn below the size of the rest of the shaft. If it's below the size of the shaft you have to weld it up and machine it back. I didn't think I would be able to weld a long shaft in the center without it bending, but a friend of mine who is a 'real' machinest said he could do it. When I went to pick it up he said he built it up with one spot at a time with the MIG and let it completely cool between spots, before doing the same on the opposite side. Throughout the day he kept adding more spot welds until it was ready to machine. It runs true, I will try that myself next time! Don't buy Chinese bearings!!
Johnny