What do you have in the /Users/jboyd/Sites/ directory? Is there a index.html or index.htm file in there? As it is now, with "-Indexes" turned off in your config, I'm thinking that Apache's trying to resolve an index *first*, before the user authentication.
First things first, change "-Indexes" to just place old "Indexes", so that automatic indexes are created. THEN try getting to /~jboyd/ and tell me what you see.
Concerning your DocumentRoot, no, an .htaccess file shouldn't be able to harm that, but using you could do some damage with your user .conf file. If the .conf file is all you've shown me here though, then it shouldn' t be a problem.
Finally, what are the contents of your error_log, shortly after you get the 403 Forbidden error message?