Misty,
The only proof of his death is an entry in the 1890 Philadelphia City directory for Richard and the 1897 Philadelphia City directory where his wife is shown as his widow, is that correct?
Whose "home" is Wernersville, the Shirley family (Richard's) or Catherine's.....? It's located in Berks County, Pennsylvania about 4 miles east of Reading. You indicate that Hains Church is where her family is buried and he's not there. What is her family's name? Nor is he in Leverington with her. Who else is buried with her?
Have you tried searching this site:
http://www.co.berks.pa.us/Dept/RegWills/Pages/Genealogy.aspxSometimes, the individual/family you are researching wasn't available when the enumerator came knocking and another somewhat disinterested/not immediate member will respond and though they try to give as factual as they believe is the family in question sometimes it's just their perception. And I assume that would be the case also when the canvassers for the directory showed up and no one was home.
What were the names and dates of the children who expired? Was it in Philadelphia?
Have you pursued the other possibility that he separated/divorced and married again? There's a real possibility there. Age of the male, county and number of years married and of course the name.
Good Luck,
Frank