You can add a separate legend for the line by using a different aesthetic to the one the current legend is using:
ggplot()+
geom_point(data=MY1andMY2_PLOT,aes(X,Y,color=METHOD),alpha=0.5)+
geom_path(data=line,aes(V1,V2, group=B1, linetype = "Myline"), size=1)+
xlab("X")+
ylab("Y")+
facet_wrap(~B1,scales = "free")+
theme_bw()+coord_flip()

You can change the other aesthetics with arguments outside of aesthetics, e.g. thickness is controlled by size:
ggplot()+
geom_point(data=MY1andMY2_PLOT,aes(X,Y,color=METHOD),alpha=0.5)+
geom_path(data=line,aes(V1,V2, group=B1, linetype = "Myline"), size=3)+
xlab("X")+
ylab("Y")+
facet_wrap(~B1,scales = "free")+
theme_bw()+coord_flip()

You can change colors by editing the color scale (red and blue are default):
ggplot()+
geom_point(data=MY1andMY2_PLOT,aes(X,Y,color=METHOD),alpha=0.5)+
geom_path(data=line,aes(V1,V2, group=B1, linetype = "Myline"), size=1)+
xlab("X")+
ylab("Y")+
facet_wrap(~B1,scales = "free")+
theme_bw()+coord_flip() +
scale_color_manual(values = c("orange", "pink"))

Edit: Change line colour:
ggplot()+
geom_point(data=MY1andMY2_PLOT,aes(X,Y,color=METHOD),alpha=0.5)+
geom_path(data=line,aes(V1,V2, group=B1, linetype = "Myline"), size=3, colour = "blue") +
xlab("X")+
ylab("Y")+
facet_wrap(~B1,scales = "free")+
theme_bw()+coord_flip()

geom_path()call. You can edit other attributes like that too, e.g.size = 3dput(MY1_DIS_REF)anddput(MY2_DIS_REF)into you question.