IMO and IMX, all of those will make a little difference, however, each one separately will not make much of a difference at all. So the real answer is, "it depends". It depends on several things: what kind of accuracy you're looking for and at what distance, are the reloads for a rifle or for a handgun, etc.?
If you have a tack driver rifle when shooting perfectly uniform rounds, then introducing any one of the factors you mentioned will most likely not noticably affect the rifle's accuracy. But, if you introduce all three variables, it might.
Deburring the flash holes can lead to more uniform ignition of the powder in the case. More uniform ignition yields a lower standard deviation of bullet speed. How much really depends on the type and amount of powder in the case.
I think your second factor, non-uniform case length, might make the most difference. If the cases aren't all the same length (and the COL is), then variations in pressure can be quite large. Differences in pressure lead to differences in bullet speed.
To my knowledge, sorting of bullets by weight doesn't make as large a difference in accuracy as you might expect. That is, assuming we're not talking about large differences, maybe 2 or 3 grains variation between bullets. Larger variations will lead to different pressures and, of course, different bullet speeds. Sorting by case weight, within a specific brand of case, might make more of a difference since case weight is usually in direct relation to case volume. If there is a substantial variation in case volume, then there will be a variation in pressure which leads to ... well, you know the outcome of that.
All in all, the biggest factor in accuracy is first and foremost the shooter, followed by the firearm, then the environment (wind, temp, etc.), and lastly the ammo (assuming relatively good ammo is used by the shooter). Only when the first three are just about perfect (or understood), will the slight variations in ammo caused by the factors you mentioned make a noticable difference.
