I have measured the runout of my 1/8" endmill to 0.001". I’m assuming this is within normal tolerances, right?. I will try different collets to see if I get different results. The spindle has no runout at all. Also, how do I correct for this in Fusion 360?. Do I just add this as an offset on my operations?. I’m doing a little maintenance on my Nomad today and checking for accuracy. Any tips would be appreciated.
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Runout is just one thing which contributes to an endmill cutting at larger than its measured diameter.
I find it’s best to just cut a series of slots or to mill out a pocket and measure that to determine the effective cutting diameter for a given endmill at a given amount of stickout in a given material.
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Even changing RPM’s will give a different amount of run out.
It’s pretty much not going to be exact (.001"), anytime you change something, until after your test run, so you can calibrate for the different materials, feeds, speeds, etc.
At least give yourself a little tolerance if possible.
My son spends hours getting everything within .0005".
Next day leans on the machine, and has to do it again.
Drives me nuts 
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Send him over, he can get my machine to 0.0005 and than go home and I’ll rope the machine off. Gotta love em huh???
my son caught 2 black tips sharks in the river last night, if he ever tries using the shapeoko I think I’d have to buy another one for me, for now it’s all mine and there’s not room for both of us in my work shop anyways, I know nuts… Jude
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Thanks, everyone. I seldom need such accuracy and the few times I’ve needed it, I’ve tested with variations of dimensions like you suggest. Mostly I’m interested in making holes that fit a registration pin to, as accurately as possible, design two sided jobs. I recently got a dial indicator and thought it wise to check for runout since I had never done it. Mostly as part of my learning process.
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