These projects almost never change the grade of the rail line; the road is either elevated or depressed to form the grade separation. At the scale of a single grade separation, it seems to be cheaper in almost every case to change the grade of the road. When there are multiple crossings in a row being eliminated, the economics usually favor an earthen embankment or trench for the rail line, or occasionally a viaduct on structure.
Central Ave at BRC (this design sucks, hopefully they have redesigned it in the 7 years since the last update):
http://centralbrc.org/downloads/
Harlem at 63rd/65th/BRC:
http://www.il43study.org/documents/