1. our current integrations work to the best of our knowledge I cant say specifically what is different an older version like 3.13
2. I think you mean upgrade.php and the directions kind of cover all versions so might be confusing a little there use to be a cookie domain in older versions that was moved to the database in later versions which is why there is a note in the upgrade documentation
3. cron.php is a new file which does the same thing as sendnotice.php which is the server cron task except it can run inline silently when someone views your page its a footer cron task much like what vb
runs with there software a silent cron to update things.