'On Top' sounds like you re-installed CSF/LFD from source.
The link you posted also suggests that.
"CloudFlare Integration" is not support by CWP at this time. I wish it was, but it's not currently.
These forums aren't for Cloudflare.
You will need to use their forums for that support.
And if you built CSF from source to add additional modules not included in CWP, you will need to use the support CSF forums for that module.