Yep, Messner, this is exactly what happens, and triggered my friend Jim's effort to make the old "electric 750". His sandcast enjoyed a less-than easy life (Jim rode hard and long), and it was specifically this difference in the holes that made him align-bore it. But...this is also common to many, many of these SOHC4 engines, in all 5 sizes that I have worked with (750/500/550/350F/400F). The reason: the cases distort over time from heat, and specifically from the top half of the case being hotter than the bottom half, causing all the tiny warpages that make them slightly misalign these 40 years later, when disassembled. That's why I advocate ALWAYS using Plastigage, and not so much bore-gage measurements, to ensure the vertical clearance (i.e., in the axis of the rods) is adequate for good operation. This is where the oil has to do its job, and the bearing joints in these engines experience almost no load (and CERTAINLY no wear!), so letting them be slightly wider will not harm the engine in use.
But...all this said: if you DO decide to align-bore them now, since the cases will not warp any more in future years, that engine will last much, much longer than they already do. And, the smoothness will have to be ridden to be believed!
On my own engine (in 2013, at 138+K miles) I went a slightly different route as an experiment, and it has turned out well: I Plastigaged every bearing (rod and crank) and selected the next size tighter-than-indicated (by Honda's rules) bearing for every site (I might add: I did this with all the valve guides, too). I then took it easy for the break-in of 1000 miles, and the power increase is dramatic (to me), as is the smoothness. There is no clearance more than 0.0009" in my engine's bottom end, now BUT...if this is undertaken, it must be done with ALL the bearings, not just the crank or the rods, as they are all fed by the same pressure stream. If one is allowed to be more than 0.0004" larger than the others with new bearings, it will hog more oil than it should and the others will all quickly wear to match the loosest one. I wanted to avoid this, on purpose: now I suspect the engine will outlive me? As a side note: the largest valve guide clearance (intake) in mine is 0.0008", some are 0.0006", and the largest exhaust clearance is 0.0018" (most are 0.0016"). No, the valves do not get "stuck" or drag, in fact they run so quiet to redline that it sounds like a DOHC engine now. I recently set the valve clearances back to OEM numbers (I have long run 0.003"/0.004" on mine) to see how quiet I can now get it to run (mine has the early-style free-rolling rocker shafts, so these do click a bit). It should be a fun season of these experiments!
