I think I can give you a little help. There is a connection between the Conewago (Adams County) Lillys and the Frederick County Lillys. Richard Lilly (b. 1728), who married Mary Elder is 1755 and settled Lilly's Lot in addition to other holdings, was the son of Samuel Lilly (b. 1699), patriarch of the Conewago Lillys. Conewago and Emmitsburgh are actually not very far apart.
Richard had a half-brother Samuel (b. 1735)but he never married and died in Maryland. Richard also had a son Samuel (b. 17590) but he married Belinda Majors Walker and lived his entire life on the home plantation.
I do not have any of the names you listed connected with the above Lilly line. Since you state your Samuel was born in what is now West Virginia, maybe they are linked with the large Lilly population in that area.