Have you tried yet looking at a history written by Rev. AJ Fretz? If the Bluffton College Library is still there they may yet have a copy of that book that had been written back at the end of the 19th century by a Myers/Stover relative.
It seems the Myers and Stover families were close in their relations and several Myers/Stover connections show up throughout the history and genealogy records as well as in the online graveyard (Deep Run Mennonite Cemetary)
From what I've pieced together from the historical accounts and what others write her of names that show up in Ohio and Indiana they most likely moved together as several members of a family travelled in covered wagons from Bucks Co. (Bedminster and Plumbstead Twp. area) to near Basil Ohio (around 1830) It's very unlikely any one covered wagon would have taken on such a long trip. It would have been much too dangerous. It was still wildnerness and undeveloped territory between civilized settlements.
I can think of many scenarios here but may I suggest you first determine if your Ephraim was actually a child of a Stover boy or if a Stover family took him in as an adopted child of their own. If that had been planned ahead of time then the child may have been given the Stover name the day he was born to spare them all from legal costs and whatever process would have been necessary otherwise for the Stover family who'd have been willing to take him as their own.
Why do you believe "John Stover" son of Rev. Daniel was his dad? do you have some proof or family story that would lead you to believe that?
From the dates you've given she was very young when she had Ephraim and she may have not been ready or willing to care for a child especially in that time when it was such a stigma to be an unwed mother. Worse yet? they may have decided it best to spare Rev. Daniel Stover and his son John so maybe a relative took in the child as their own? to raise him in a place where nobody would know him or his mother? or who his father was?
the whole community may have rallied to spare her the embarassment or a "shunning" from others who'd have considered her unworthy of them.
Times have changed greatly since the time your Ephraim was born so it might be very difficult to find anything other than church records that would have Ephraim as part of a family of Stovers in either Pa. or Ohio when he was a child.
what about his marriage certificate? does he name his parents on that? I guess I feel a little confused as to how you have the information to begin with that he'd been born out of wedlock. Was it from a birth certificate only?
I don't think our Issac Myers was his father because the date of your Issac's birth but it is very possible a close relative to both the ancestors we have travelling across the Alleghany mountains sometime around 1830 (Michael Myers and Rachel Kratz Myers, daughter of Jacob and Elizabeth STOVER)could have been instrumental in getting the young couple and Ephraim to a place where they'd not be subject to a community where everyone had known their "secret"
I am running into this kind of thing in my more immediate family with relatives a whole lot closer to our more tolerant generation than the ancestors had been.
Hope you find the truth you are looking for. I'll be in Pa. this coming weekend and searching Stover/Myers records. If I come across your Issac will let you know.
if you haven't yet found firstname.lastname@example.org