If you're interested in an alternative way to do this you could consider Certify The Web (https://certifytheweb.com) which I develop. The reason I suggest that is your problems seem to be centered around Windows file permission and symlinks, which are avoidable with an alternative client and in this case the client is built specifically for Windows (usually for IIS but it can be used with Apache).
To do the same using Certify The Web, with "standalone" equivalent, or alternatively using the "webroot" method:
Getting a Cert
- Make sure nothing is currently using port 80 (e.g. apache)
- Use New Certificate to setup a new managed certificate, add your domains, click Request Certificate to try getting a cert. See Requesting a Certificate | Certify The Web Docs - If that all works proceed to deployment.
To alternatively use a "webroot" method instead (serving the http challenge via apache instead of using the http challenge server built into the client), set an output path for the challenge response files pointing to the root structure of your site, under Authorization > Http > Site Root Directory. Ensure that extensionless files written into /.well-known/acme-challenge/ can be browsed to over http. You can use "Test' to check if challenges are being served ok.
Deployment
Once you have your cert you can use a deployment task to place the cert files where you want them (e.g. C:\certs\nimoweb.ddns.net) and restart apache.
You normally would set the fullchain.pem path and privkey.pem path, then save and hit 
Play next to the task to try it out. This should give you the output file you need in the location you want. You then just need to point your apache config at the right files. You can refine this task configuration and test the task without re-requesting a whole new certificate.
You would normally need a Deploy to Apache task and a Stop/Start/Restart service task (for apache).
Once you have these setup your subsequent renewals will be automatic.
The benefit of separating the process of getting your cert and deploying it is that you can troubleshoot them individually.
[Edit: I've updated our docs for Apache/nginx deployment : Using with Apache, nginx or Other Web Servers | Certify The Web Docs for future reference]