Hi
Hope your cold is getting better! I've had a sprained thumb so not been doing much on the computer either

I've been dipping in and out of you posts and you certainly have a knot to untie what with name changes and so on. I know you have a ton of information now so probably anything I say can be discounted easily, but here goes just in case even one idea helps.
1. I just can't see that a Charles Ashby married Mary Ann Sears in 1852 at St Botolph (extracted record IGI) and that another entirely different couple with the same names married 100 years earlier (your records). But if you have seen the entry in the records then I must be wrong. From this distance it looks as though the marriage you have for Charles to Mary Ann, and the baptism of their son Charles have been mis-recorded a 100 years too early.
2. I don't understand this bit:
"The earliest Charles Ashby is the one whose birth record I need to trace to establish his parentage: (his father was thought to be a Richard Ashby of Eagle Street, Picadilly, London, died 1789 aged 60 but we cannot find a death record anywhere for Richard Ashby although I have managed to find him mentioned by name and address in the rate books for Westminster for the year 1780,
so I know he existed but why no death records anywhere?) He is reputed to be a son of the Ashby of Harefield line who converted to catholicism changed his name from Robert to Richard Ashby and died in 1767 without issue ie was dead to his family for converting but secretely married and had issue but was cut of of his fathers will anyway for converting to catholicism and his father Robert Ashby senior left everything to his daughter Elizabeth."
I can't quite work out who died when. The NatArchives has wills:
1767 Robert Ashby of Custom House London
1769 Robert Ashby of Harefield
then there is a record ACC/85/343 15 June 1762
which talks of Robert Ashby snr of Harefield and Robert Ashby jnr of Custom House so are the two wills for father and son? Did the son Robert die in 1767 before is father or are these just probate dates so his father died first but not probated until after?
You said somewhere that Edward Ashby said his grandfather "on fathers side was an unbeneficed clergyman called Richard". I can't mesh that with the idea of Robert Ashby converting to Catholicism and changing his name to Richard.
3. I noticed that you give the marriage for Edward Ashby to Elizabeth Eyre at Well Street Chapel in 1813. It also took place 26 April 1813 at Saint Benet Fink, London (IGI), I think it needed to be in a parish church to be legal. Does that entry have any details different to the chapel one? I doubt it but you never know!
4. Very interesting family you have! I found some stuff about Elizabeth Eyre's father - you probably have it already
http://www.british-history.ac.uk/report.aspx?compid=22714I wondered if Charles left everything to his 2nd wife because Edward was financially settled? But perhaps he was miffed if he had become a dissenter.
5. Edward's brother Francis Jukes Ashby - do you know where the Jukes comes from?
Not helping am I?

This is my 3rd attempt to post something sensible so I will post it, sensible or not!