How to set new identities for new clusters based on a gene expression in Seurat?
You have to define your ident it has to have the structure of a table. You put the cell names as names and clusters as value (for instance cell 1 = YEPF+ cell 2 = YEFP-):

pident=as.factor(clusters)
names(pident)=cellNames    
object1@ident=pident


Then you can run the FindAllMarkers function on this object:

FindAllMarkers(object1, min.pct = 0.25, min.diff.pct = 0.25)