Thing is though, the cams are theoretically asymmetrical so all things considered, it should be fine. Even eyeballing the cams themselves, they're pretty much identical, just a slight bit more lift. Ideally yes they should be timed to one another and run on a dyno to see what's effective but I don't have the time and money to invest in something like that.
I have something done similar to the intake cam of my VW where I use a modified exhaust cam as the intake. Timing unmodified and just dropped in, it worked fine all the way to the 7200rev cutoff but when the sprocket was brought in to smooth the overlap, the cam became mush smoother though the top end hit wasn't as pronounced.
The only thing I can think of is that the lift may be too great for the rockers (since the exhaust rockers are different: thicker versus the intake) and at certain RPMs may be floating. Could even be coil bind at those revs due to the rockers/lift/speed (I haven't the time nore the machine to check springs). Something to compare to existing camset #'s out there to see if that could be the case.
I wish I knew someone with a boroscope because that would answere alot of questions quickly. Since everything is so damn small, it's almost impossible to peer down the plug hole down the piston to see if there has been contact but I also believe if they've been touching, something should have let go by now. I mean, the plugs even look fine.
There are lots of variables in what can be causing the "rattle" and I think that it could even the be the cam chain as well. Things turn over fine by hand and I have run the thing to 14ks with no real ill effects. All the marks line up and it fires up as if it were stock so I really don't know. It's going to have to wait till I get a couple of more miles on it and peel off the VC and check tolerances etc.
The joys of experimenting and tuning. Like I said before, I'm happy with it as it's made the bike more rideable for me but what works for some won't work for others.
If you have a chance to get over to SVRider, this is apparantly a pretty hot-shit mod for them and they even use cams across generations looking for the correct lift and overlap. Interesting reading there. They've got dyno plots to prove it and like anything, without changing displacement, all you're doing is idealizing what you have and you'll lose/gain in different places, moving the powerband around.
One also has to remember that the stock cams are what Suzuki thinks is the most ideal for the broadest range of what the bike will be used for. It may be tame but it's the most consistant. Anything else outside of the prescribed box has to comprimise something.