You will either end up with an ad hoc, informally-specified, bug-ridden, slow implementation of half of SQLite ... or, you will fail to even attempt the features that SQLite gives you - such as locking and dealing with concurrency - and you will have bugs.
For example, you use file_put_contents. See this comment: http://www.php.net/manual/en/function.file-put-contents.php#...
Please don't go and add locking now! (It's hard to get right). SQLite was invented to be a better fopen() - use it! There is no reason not to, if you are requiring PHP 5.3. If you want a simple plain text dump of your SQLite DB, that's not hard to add.