Northerners are not homogeneous, so you'll have to specify.
There are Nilo-Saharan Northerners that are related to South Sudanese; and then there are Sudanese Arabs, Beja and Nubians that share absolutely nothing in common with Southerners.
Generally, no. The Nilotes of Blue Nile State are the exception; the 'Nuba' are not even closely related to South Sudanese as most of them are Niger-Kordofan speakers.
The indigenous Darfurian tribes (Fur, Masalit and Zaghawa) are Nilo-Saharan, but they're also different to Dinka-Nuer peoples.
No, it's the complete opposite; there is virtually no genetic, linguistic or cultural difference between a Isaaq man from Hargeisa and a Hawiye man from Xamar.

Never knew Sudan was like this