(1) creating an identifying mark that
Oh, right. God couldn't come up with anything better than "cut off part of your penis to show people you are mine". Kind of like a primitive divine game of "you show me yours and I'll show you mine". If that's the best god can come up with, it explains a lot.
also served as a means to save a nomadic people who (a) had little water to expend on bathing and/or other water-dependent hygienic activities, (b) lived in [often very] close proximity to their livestock... many of which were sheep ... and (c) often had multiple wives and/or sex partners (the latter of which sometimes included the livestock)... from serious and potentially epidemic STDs.
Ah, you are appear to be sufering under the delusion that having a foreskin is somehow less hygenic that not. How incorrect of you. Besides which, how foolish of god to ever create one in the first place.
Ohhhhhh, you meant do with them... as in after they were removed. Answer: the same thing they do with them now.
Come on, God asks for them from adult men and his best idea is "whatever you'll do with them in 4000 years"?