Thanks. I've never had an issue with Toolkits, I can see where things would go wrong, but I don't rely on them fully. I am aware it's all pretty much ADB or FastBoot commands that you're running. I like them for confirmation of commands or just as...
So I have ended up keeping S-Off since there's no indication that I could 100% S-Off later according to their F.A.Q.
However if anyone else was thinking of doing the same, I did just have to change CID and MID then used the HTC Stock T-Mobile RUU...