Not so paranoid,
Opening files in a text editor should be safe. Opening other file types is more risky, PDF's, images, office documents, have all had vulnerabilities where opening the file in certain viewers. Most text editors are simple enough that they have few vulnerabilities.
Ensure you never run the .php files, I would recommend changing the file extensions to .txt as soon as you download them.
Extra step for the paranoid, I would also recommend opening the files in a simple text editor, like notepad, editpad pro, sublime text or similar. The more complex and the more the editor understands the format the more likely it is that there is a bug which could be exploitable. This is much more a problem with complex formats like .doc or .pdf.
There is the academic answer and the pragmatic answer and they are different.
The academic answer is that it is possible that opening any file in any editor could compromise your box. It is possible that copying the encode text into your paste buffer compromised your box. It is possible that pasting the encoded text into a website compromised your web browser which compromised your box.
The academic answer is not very helpful.
The pragmatic answer is, you'll be fine as long as you did not execute the files. Though the academic answer is factually correct, it is highly improbable the attacker the compromised the server either had access to or was willing to use zero-day attacks against desktop software.
For next time you are doing incident response or malware examination you should consider doing the work in a virtual machine, and discard any changes to the virtual machine once you are done with a piece of work.