I wouldn't use "over" in #3, so that's one difference. Also, consider using "went" instead of "came" in #2. I assume you know the difference between those.
In addition, I consider "come over" to be more friendly than "come up". For example, if you're inviting someone to your place, it can work better.
A mother might say to her child:
Go and ask little Vanessa from next door if she'd like to come over and play with you for a while.
"Come up" wouldn't work as well in that sentence.

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