I've no idea about cloudflare integration, but there are many ways to protect server from DDoS attack such as block known malicious IP and limit request amount.
Well, I don't have much knowledge of other software only Cloudflare that I know to use to protect it from DDoS attack.
I don't know but it might be possible?
Temporarily I'm using https//coinb.in for making transaction from electrum offline and get hex then broadcast it to coinb.in just to make a transaction.