We had similar issues with a unix forwarder. I has to monitor over a million of files. It stopped sending logfiles and had high CPU consumption. I assume you are struggling with the same issue as we did.
The UF doesnt like haveing lots of open files like you configured with alwaysOpenfile=1 Even if you get rid of this option I doubt that the UF will work.
Try using the batch://option. It reads and deletes the file. if you dont want to delete the file on your server I suggest, that you write a script in which the files are copied to a temporary directory.
In the end you will have configuration like this (inputs.conf):