I tried a set of x links on my r which does raise it up a couple of inchs but then I found I couldnt reach the floor properly as Ive only got little (stumpy) legs. I found I was having what I would call comedy offs where I was dropping the bike because I couldnt hold it up when trying to reverse or manouvre in tight spaces or on a failed hill climb etc.
If youve got long legs it probably wont be a problem.
The only issue Ive had with ground clearance was hitting the bash plate into the ground and because its made of toffee (the yam one) it kept denting into the exhaust pipes. Ive fixed this by changing to a two into one system so the exhausts are out of the way. Now it doesnt matter if it bottoms out.
The standard shock/spring setup has worked fine for me and what I do and the only change Ive made to it has been to fit fork spacers which has taken some of the braking dive away and firmed the front end just a little. I can and often do ride hard off road in fairly challenging terrain with good response from the bike. Ive not had problems with suspension bottoming out and Im 16 stone. I have the preload set just over half normally and a notch higher when loaded up with camping gear and or wife. I personaly have never felt the need to start changing suspension as in my own opinion if I need to do that its time to change for a wr or similar.
A bit long winded I know but hope it helps.

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I'm always in the sh1t, only the depth varies