i *think* you can flash mr2 overttop of a custom rom without a SECURITY WARNING but ive never done it,so try it at your own risk.
what i HAVE done successfully is pull the hboot from the MR2,flash it,then flash the hboot last just as reccomended with MR1 in the OP. i could prolly upload the files if anyone wants them(its easy enuff to modify on your own). saves the phone from having to OTA after your done.
since MR1 isnt the latest firmware and its going to OTA anyway,you could also just flash the shipping firmware(1.12.605.6- doesnt cause a SECURITY WARNING) and then let that OTA to mr2. simple unroot!
what i HAVE done successfully is pull the hboot from the MR2,flash it,then flash the hboot last just as reccomended with MR1 in the OP. i could prolly upload the files if anyone wants them(its easy enuff to modify on your own). saves the phone from having to OTA after your done.
since MR1 isnt the latest firmware and its going to OTA anyway,you could also just flash the shipping firmware(1.12.605.6- doesnt cause a SECURITY WARNING) and then let that OTA to mr2. simple unroot!