We have fastboot files now, so you are OK to mess around, but at the same time, it won't be an issue.
I use the Droid4 utility, and it's been very clean for me. I couldn't get Motofail to work, so I would suggest the Droid 4 utility.
As for safestrap, I had this issue, and when I put it back, it installed correctly, and there were no issues whatsoever.
Ok I'm rooted again, thanks. I'm in safestrap and it says 'Recovery State' is already is installed, should I uninstall recovery? Thanks for the help too guys.