Try this company.
http://tsukayu.com/products.htm
I'm looking at the patrol bags from them and in talking to them they say that it might be close with the stock pipes but there won't be any issues with heat.

 

I have hard bags over my exhaust. There's about an inch of clearance between the exhaust and the bags, plenty of space. If you're really paranoid, bolt a piece of aluminum to the under side of the bag. Will be out of sight and will protect the bag from heat. Has worked well considering my pipes end right under my bag, they don't even go all the way to the end so exhaust is hitting the bag. I've had no issues thus far.