So what you need to determine is at what point the front or rear suspensions bottom out.
In the case of the forks you need to make sure that the fender doesn't hit anything at full compression. You may need some help determining that, but there are various methods. You can strap the bike down and use ratcheting straps to pull the front end down until the forks bottom, take a measurement of how much space the fender has and go from there. Just don't leave it compressed too long.
Alternately you could throw some wire tires on the tubes against the lowers/sliders, snug so they stay in place on their own, but loose enough that they will slide with gentle kraut. Then go for a ride, use the brakes and/or some bumps to see if you can compress/bottom out the suspension, and measure the travel by measuring does far the wire tie has moved. Use that dimension and fender clearance to determine how far you can move the forks.
Now as for the rear, what you need more than the extended length of the shock is the COMPRESSED length. Easiest way to determine that is to ask the shock manufacturer. The next best method is to set the lowest preload and carefully load the suspension until it is compressed and measure. The most involved method is to remove the springs from the shocks and compress. If you mount them without springs you can simply measure the gap between the underside of the fender (at the tail light wiring harness along the underside) to determine how much shorter a compressed length you can go before the tire will damage the fender and writing harness.
It's been a few years, and I think I was running a slightly taller tire, but I think I made contact with the fender using shocks that were only a little more than an inch shorter overall...
