The requested URL was not found on this server

Are all of your filenames like how the userguide specifies? Windows doesn't care about case sensitivity for filenames, but just about every other OS in the world does.

You might also try adding a ? after index in this line:
RewriteRule ^(.*)$ index.php?/$1 [L,QSA]

I will check that, I moved the site from one.com to my windows machine. I remember when I renamed a file, first letter changed from or to uppercase, that on windows I saw 1 file but on the file manager of on.com I saw 2, one with uppercase and one with lowercase.