All server files are relevant except for config or user-dependent files.
strip the mtaserver.conf, acl.xml, vehiclecolors.conf, banlist.xml, internal.db, all database(s) files, local.conf, mapeditor.conf, resources dir, (you don't want your current scripts overwrited with MTA's default)
Simply take a server-only install in another directory, remove above files from it and apply the update to your server by pasting them into your server's directory and overwriting the old files. Make sure you backup these old version's files, before updating, ofcourse.
Latest release is at the homepage but I recommend keeping an eye at the nightly page for this, where CiBer linked you to.
(https://nightly.multitheftauto.com/)
You can take the latest 1.3 nightly there, and as an indication of the correct file as you couldnt see it there yet, it looks like this: [version/date] mtasa-1.3.5-rc-xxxx-dd/mm/yy.exe, or full if you dont have all server files yet (mtasa-1.3.5-full_rc-xxxx-dd/mm/yy.exe) which is the format of the right files you need to get, and to be found under 1.3 - Current release version while scrolling down that page.