All of these sentences are grammatically correct, but there's more than grammar.
“Is everything okay at your place?” is idiomatic. “Is everything okay in your place?” is not. When place means home, the normal preposition to indicate a current location is at.
Let's go to your place.
I'm at her place.
It takes half an hour to go from her place to mine.
While “in your place” is possible, it isn't common; in cases where the right preposition is in, the idiomatic phrase would use a different word: “in your house” or “in your apartment”. One reason “in your place” is rare is that “place” tends to have fuzzy limits: it means the location where someone lives. If the walls that separate the location from the outside are important, it is more common to use more precise words such as house or apartment. Another reason “in your place” sounds weird is that it usually refers to a completely different meaning of the word place: “in your place” means “if I were you”.
On the other hand, “on your end” and “at your end” are both idiomatic and pretty much synonymous. US English favors on while British English favors at.