Are you bottoming out the forks, rear suspension or both? I am around 185lbs, no bags (on the bike anyway!) and I've never experienced this. Or do you mean the big rocks are striking the underside of the bike?
Ted: this is the wrong bike if you intend to spend a lot of time with big rocks. You'll need a bash plate to protect the bike if you spend a lot of time going over big rocks, unfortunately, that will lower your ground clearance a bit!
I already have the plate and it runs nice across the rocks as long as you ride the pegs. I'm taking rocky roads; we have a lot of old mines up in the mountains. I found links that will raise it an inch; I just wonder how that will effect the tight corners getting up the mountain to the dirt roads. It's a 650.
Raising the bike will cause the most problems with getting on it and touching the ground. You can only raise the bike up so far , the forks in the tripple clamps are the limiting factor. You do not want to put the tail to high with the links. Maybe a 6mm to 10 mm adjustment on the hole lenght of the links measured between the holes. I laugh going from my SV1000S to my Weestrom the feeling of leaning the taller bike over is a blast.