Well it looks like my theory about Johnson Williams being the father of James is right, I found a DNA match on ancestry that appears to be a cousin through Johnson's father. it looks like Johnson is the son of Burrell Williams and Polly Morris and my DNA match is a descendant of Burrell. in theory this seems to confirm Burrell as the grandfather of James Henry williams and father of Johnson Williams.
while I know that James is my line without a doubt, Johnson now seems to be his father and Burrell his grandfather. hopefully some kind of records will appear some day some where some how to confirm this theory.
also, I have a theory on James' mother Malinda. and this one may be wrong. it may be very wrong or it may be right. it's almost too speculative to believe. but here goes, someone said that James was Blackfoot.... and maybe so... or maybe his skin was darker because his mother was Blackfoot. still have no records on her, but a theory of a cousin is that she was born Malinda Mills and she was a person of colour. really wish I could confirm that. apparently she may have been a native American or an African American. a record found says that she was black and she married a Williams later she married a Smith and lived out west. now if James was mixed then he could have had lighter skin toned kids right? I found a picture of his daughter and she looks pretty white so I don't know. if she was say a quarter native it may not look that way I guess.
so this cousin found a record some where apparently that Johnson did in fact marry a Malinda Mills and she later married a Smith. so the paper trail looks pretty solid. Malinda could have married Johnson to have James then left with him and remarried. while there is no record of a James williams in their home they in fact, did have a James Smith living there. could this Malinda smith be THE Malinda smith who was the mother of James??? sure could use a flux capacitor right now.
any way I am pretty confident about James father being Johnson Williams now and I know for sure his mother was Malinda smith. but was she Malinda Mills? that's the question. this line has been really difficult to find and I hope it's right now.
i know James was my ancestor and am pretty sure now that Johnson and Burrell are too. Malinda Mills? maybe so. but some sources would be nice to have for this theory.