Some hotly debate some of the replacement rods being a smidge too short or long but any competent wrench can easily compensate for that little issue.
Could you quantify "smudge", I could live with a little less compression (minus smudge) and some kind of spacer under the barrels to stop any valves assisting the piston to return, anything more complicated than that is beyond this Wrench 
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I avoided specifically quantifying Smidge, Smudge, Gnats A**, Skosh, C**t Hair-defined by blond-Ginger-Brunette, Inch-thous and "Metrification" because off the top of my head I would probably misquote or say something stupid, Here on this discussion, or the others where the length of the rods are debated.
But its simply good practice to mock up a motor and check ALL your measurements before final assy and adjust accordingly. when it comes to Ass-U-me that dimensions are correct, you will usually be disappointed on these old engines. Has the head ever been skimmed? (Has anyone ever done a survey of cyl heads & cyls for dimensions to see how consistent they are??) What about the cylinder surfaces? Unlikely but possible but crankcase deck surface?
List is long on the possibilities, but Thicker/thinner head gaskets, base gaskets & spacers, Milling piston tops or opening valve reliefs are all typical, and then dealing with related geometry issues.
(Pushrods, cam followers, rocker arms) Depending on the math, a INCREASE in compression might be a good thing if alloy head. Check ACTUAL compression, not theoretical. One point often overlooked is in some cases one cyl will differ from the other in actual compression.
These were pretty agricultural motors and close enough is good enough was the norm.
Optimizing IE: Blueprinting is advantageous in many ways.
Short story: My good friend Sir Eddy was a english immigrant who upset the local racing scene back in the late 1950s and early 1960s here in the PNW. He had the first Norton Manxman in the Western US ordered in specially for him. He immediately took it apart and blueprinted it stem to stern. No fancy bits, no secret factory speed parts, and while he chatted often with Paul Dunstall (taught Paul some things and learned some things) all he did for cams was offset ground the stock 650ss cam to get a tad more lift, Did a little port work and then balanced it.
When Eddy was done, The motor was so perfected and dimensionally correct it was virtually unburstable in racing. He took records in Drag racing (Sprinting, 1/8th mile & 1/4 mile) as well as road racing from Westwood, Seattle, Portland/PIR and a few trips to California. They even took his motor and stuck it in Sonny Burres's flat tracker and won a AMA National race and spanked the Berliner Norton factory riders.
In short, that 650 was the fastest thing around and faster than factory racers.
After Sir Ed quite racing a local shop (Dirtbags-Glen Adams) bought the motor to see what magic was inside.
Sorely disappointed and quite angry. No super speed parts. Blueprinting was the secret. Norton stuff is very crudely made, (Sorry-
BSA as well) and optimizing specs pays huge rewards.
Here is a picture to illustrate. This is Sir Eddy at Westwood, So bloody fast the blighters goggles flew off and note he is pulling air on that front tire while accelerating.
