I have not forgotten about helping you! I have been doing a little digging on the internet, and some more at the Warsaw Library, and then more at our local historical society... they have a nice collection of records, too.
I just found your family tree online at Ancestry. Very Nice.
Given the marriage records and ages of Mary Silver, I doubt she was James Clarence's mother. My guess is that Mary Silver is a second wife.
James Hall marrying Mary Silvers on 4-28-1859
(J.G.Watts - Justice of the Peace)
Knowing (assuming) that James Clarance was born in 1855, I looked for obvious marriage records for his parents in the preceeding years... not much on record before the WPA project of course, but some stuff. I could not find anything. I searched death records and cemetery listings to find a female Hall that passed away between 1855 and 1859... nothing really fit.
Another option - Since James Clarance (JC) is not in the James Hall/Mary Silver household in the 1860 census COULD MEAN... his mother left and remarried and took JC with her... and your JC may have been recorded with a different last name... maybe for years. I like to think outside the box some to give me more ideas where to look for clues!
Anxious to hear from you!