Her naturalization documents confirm the name of a ship, port of departure with her NY EI arrival manifest. You are saying that on her naturalization only Minsk and not the [mis]spelled location Jakuslkj, Russia. I sort of thought that the location might start with a Z in the place of birth but than on the last residence it looks more like a J.
The children's church baptismal record should have mother's place of birth.
Yes, I saw that her father's name is Jacob which could be Jakov/Yakov/Aykow. to translit the surname into Cyrillic http://translit.cc/http://translit.cc/
Can you follow the paper trail of the brother-in-law she was going to? Might we assume that the other 3 passengers traveling with her were knew each other? After all they were from Minsk and gubernia Minsk but I can not decipher their locations to try to find Matrona's.