Just wanted to let everyone know my process. Worked great thanks to Chainfire's genius.
My starting point
Bell I9100M upgraded to ICS LD3 official release through Kies.
I went through the CF-Root process and used LP7 (the second link in the list but I don't think it matters). You end up with a rooted kernel with CWM and the ugly yellow triangle.
CF-Root 5: Upgrade Firmware feature
Using this feature I was able to get my LD3 firmware back with root and no triangle. I created a folder on my external_sd called "firmware" and put the stock Bell LD3 firmware from Samsung Updates in there.
I then opened CWM and selected Flash Stock Firmware and selected the stock firmware. I continued through the prompts about the bootloader and then selected the pre-root option.
After boot I had LD3 rooted and working perfectly with no triangle. I have no idea whether it actually reset the flash counter but I'm okay with this solution for now.
Also, because I went back to the stock kernel CWM has lost snazy features like Flash Stock Firmware but I'm alright with that for now too.