I wrote before with your setup you don’t need to change the yaml files. Only enter the IP.
Where are your scripts at the moment?
Don’t touch MRPE, all your scripts from your config file before where normal plugin scripts.
Give us some information what you see with a clean agent install in your discovery.
Put only one of your checks inside the folder “C:\programdata\checkmk\agent\plugins”.
Check again your discovery. Remember that it takes two times of the normal check interval or two full scans to get the actual data as all plugins are in asynchron execution.