I would try a ratchet strap instead of the bungee cords. That should help keep the back planted since there will be less play. Of course just snug them up, so the wheels aren't damaged.

 

I would imagine that would greatly improve the stability. If I was going to attempt this again then yes I would likely run one of the two flat bars all the way out to the Bak's mounting bolt in each corner. I'm pretty happy with the outcome though as it sits. It's way more sturdy than most roof racks I see on a daily basis.

Shockingly, I'm not even sure the bungee's are needed. I'm pretty confident that you could go down the road and each tire would stay relatively in place. The bungee is VERY light and just gives me good peace of mind in the corners that the back end of the bikes won't shimmy and slide towards the bedsides. The ratchet strap would be overkill and in my eyes, a little unsightly. To me the small bungee is aesthetically pleasing.

 

Yea I was concerned with taking corners and the bike pivoting on the fork and sliding off the cover

 

That's what I'm thinking about. A hard right turn pulling out in traffic can cause stuff to slide around quite a bit. I don't really worry about it when my bike is in the bed. The skinny road bike tires fit in the groves in my bedliner. On tip of the bed a slide could tear a lot of stuff up in a hurry.

 

I ride 3-4 times a week. Sometimes 30 miles from the house or more. The bike might move 1" left or right and it's showing almost no sign of wear on the cover. I also love having full use of an enclosed bed while carrying the bikes.