Vesta CP, Cloudflare and Let's Encrypt: Wrong folder and error

Question

I am facing multiple issues with my current installation of Vesta CP on my VPS. Trying to switch from normal webhosting to a VPS, but it is not going good so far.

Issues:

1. Cloudflare or Vesta CP points to the wrong directory, when I disable the proxy mode and switch to only DNS.
2. LetsEncrypt is not able to generate a certificate because of "Not Authorized" error. However, I could do this for another domain.

Issue 1 Currently, I am using the following setup: Registrar -> Cloudflare (Proxy) -> VPS (Vesta CP) = Everything is fine.

When I try to switch of the proxy mode: Registrar -> Cloudflare (DNS only) -> VPS (Vesta CP) = It points to another website, so two domains point to the same place, which is not what I want.

Any way to run Cloudflare (DNS only) and make Vesta CP point to the right directory?

Issue 2 I have Letsencrypt installed and am using it with another domain, where I have Strict SSL in Cloudflare, and I get no errors at all.

When I try to create a SSL certificate for my second domain, I get an error (Not Authorized, the challenge did not match...).

I want to have Strict SSL with cloudflare for the second site, and therefore I need a SSL certificate.

Help Does anyone have the knowledge to help me fix these problems? I would appreciate it. I have tried many things for hours, without any solutions.