Not only the alignment or the correct spacing but also the damage to stubborn spacing rings and threads, the quality of the air (dust) in your room (something you're concerned about a lot...), its humidity etc. It's not for no reason that assembling lenses is done in a strictly controlled environment and with a plenty of special equipment at hand. Unless you have all that and the know how then to disassemble a modern lens means to lower its value and performance.
Once I gave a lens for cleaning of some internal dust to a firm that was doing that. When I got it cleaned and commented on the presence of some residual dust in it the technician told me - that I cannot do as we don't have the sterile rooms they use for assembling of these lenses... In hearing that I appreciated his honesty....
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