How are you supporting the bike?

Just making sure it's not on a triple stand.

Also, remember you're losing a ton of leverage not using a clipon to move the triples.

 

I had the same problem on my FZ when I changed the steering head bearings. Same procedure and pretty much the same torque values. 13 lb/ft on the second torque put too much bind on the forks when turning them side to side. I undid the nut and re-did it until it was torqued to where I was satisfied with the side to side motion of the fork. After about a week, I had to torque the nuts again because everything settled in and I actually had some free play in the head. But even then, 13 lb/ft was too much torque. My bike was supported using two jack stands and a piece of rebar through the engine mounts. Not sure if you can support the R1 the same way.