404 Errors after turning on SEO URL and Secure URLs

Question

Initial Setting:

1. HTTP only
2. SEO Url Turned off

What was changed:

1. Turned on SEO Url to remove index.php from Url
2. Turned on SSL for Admin and Frontend.

Issue:

1. 404 Error messages
2. Unable to login to magento admin

Resolution Attempt:

I tried to reverse the changes that i made, as i was unable to access admin. I did it through database, phpmyadmin.

1. Restored the Base URL settings in core_config_data set: web/secure/base_url to http://www.domain.com/ web/unsecure/base_url http://www.domain.com/

2. Turned off URL Rewrites from database: set value for web/seo/use_rewrites to "0"

3. Turned off SSL for frontend and admin web/secure/use_in_adminhtml 0 web/secure/use_in_frontend 0 web/secure/offloader_header SSL_OFFLOADED [this is as originally]

4. Cleared var/cache and var/session removed the contents of both these folders.

5. Reindexded the Catalog urls by running php -f indexer.php -- -reindex catalog_url

Current State:

1. Homepage loads fine.
2. Product URLs do not have index.php in them. causing 404. When i add index.php in the url the product loads fine.
3. Some menu items on homepage have index.php vs some don't.
4. Admin: goes forcefully to https
5. Admin:404 message. the url forces to https.
6. htaccess file remains unchanged, i have checked with a diff of htaccess backup.
7. Htaccess rule for enable rewrite is as "Options +FollowSymLinks RewriteEngine on"

Will appreciate help to have this fixed.