can you get into the admin side, your http://domain.com/wp-admin
Delete the .htaccess file entirely and you should be able to access your site. You may then want to create an empty notepad file, rename it .htaccess upload it to the root of your instal and then update the link structure while you are in the admin area. Create a new page and if it comes down to it, set your .htaccess to 777 just to see if it will write the page to the htaccess file.
Then set the htaccess back to 644 and see you can view your site and view the pages.
I've not had an issue with htaccess myself, with some exceptions, but nothing that would cause my site to start pumping out 404 errors. There are some weird things that do happen, and sometimes it can be host related in that you have to set your htaccess higher then recommended in order for it to work on certain hosts