Rear Wheel Removal
You'll need a six-point 46mm (1-13/16-inch) socket and a torque wrench with a handle extension. Most sockets this size are 3/4-inch drives so you also may need a 3/4-to-1/2-inch drive adapter. A 12-point socket will work too, of course.
Check your socket's construction. You may need to machine down the hex end face of the socket if it has recessed flats. Otherwise, you'll only get partial engagement of the socket flats on the comparatively thin nut. There's high torque involved here so you'll want to anticipate slipping and damaging the nut.
The rear wheel is held on with a 46 mm nut cross-drilled to accept a safety retaining clip that is installed as a safety precaution to prevent the loss of the nut. If the nut was not torqued correctly when last installed, the nut may have loosened a bit and captured the pin. This will prevent the socket from being placed over the nut, so you may have to cut off or pry the pin out.
You can expect that the rear wheel retaining nut will be VERY difficult to remove, usually requiring the use of an impact driver (or a long handle extension) to get it off. Over time it seems to get tighter.
A good way to keep the wheel from turning while removing the nut is to have a helper apply the rear brake lever with a normal amount of force. Be careful, too much force on the lever can break the rear master cylinder bracket which is the pivot point for the rear brake pedal.
Rear Wheel Installation
A Ducati tech bulletin and their web site specifies 176Nm ± 5% (9Nm) torque requirement for the rear wheel retaining nut (normal thread direction). This converts to 130 ± 6 lb-ft. This value is based on using grease on the threads (this is not optional.) The manual calls for Shell Retinax HDX2, an automotive grease.
In general, a thread treated with either an anti-seize or a lubricant requires a lower torque value (than a higher-friction dry thread) to create the same tension in the fastener. So, if you have changed to a titanium nut, such that anti-seize is now needed to prevent galvanic corrosion, you'll need to torque the fastener to a approximately 10% lower value to avoid over-tensioning the fastener. A new torque wrench is probably accurate to ± 3%.
When reinstalling, first make sure that the wheel is seated properly. Mount the wheel and tighten the nut to about 50 lb-ft. Then rotate the wheel and pound the side of the tire with the heel of your hand in several places around the circumference to seat it. Then tighten to about 80 lb-ft and repeat, applying the rear brake lever to keep the wheel from turning. Finally, tighten the nut to 124 lb-ft and check the retaining pin hole alignment. Torque again as high as 137 lb-ft to line-up the holes and insert the retaining pin.
If the nut is under-torqued it will allow the nut to loosen, allowing the wheel to rotate in its mount and be damaged by repeated acceleration/braking impact loads that will ovalize the four locating pins holes on the backside of the wheel. Damage to the axle spindle can also occur. Also, a loose nut will back-off till it's stopped by the retaining pin, then bend the pin and deform the nut. It's a good idea to mark the nut position with a marking pen, so that you can quickly see if the wheel has moved after a ride.
DURING INSTALLATION, YOU SHOULD NEVER LOOSEN THE NUT TO INSERT THE PIN. The range of correct torque values for the nut is 124-136 lb-ft so the correct procedure is to torque to the lower value, check for hole alignment and torque up to the higher value if necessary to align the holes.
Note that if you are installing aftermarket wheels, a small variation in wheel/paint thickness may make it more difficult to apply both the correct torque and also get the correct hole alignment.
Here's the important part. Ride the bike and recheck the nut's tightness. It's not uncommon to see it loosening up just a hair after the initial tightening. It's a good idea to mark the nut position with a marking pen, so that you can quickly see if the wheel has moved after a ride.
Front Wheel Removal
First take the big end nut off. Then you can loosen the axle clamp bolts on the forks.
There's a tool that fits inside the right hand end of the axle that comes in the tool kit. It looks like a short piece of tubing with a couple of holes in it and a couple of pins sticking out on opposite side.
Stick this in the right side of the axle and with a rod or screw driver through one of the holes wiggle and twist the axle out. The fit of the axle in the front wheel bearings is snug. It helps to support the weight of the wheel as you slide out the axle. If necessary, you can fabricate a dowel rod of wood or plastic to help tap the axle out from the left side.
Front Wheel Installation
If you don't follow the proper installation sequence, you can incorrectly align the front axle in the forks. Also, be particularly careful when you tighten the pinch bolts - the Ducati axle is thin-walled and will ovalize if these bolts are over-torqued.
You can use a dowel inserted from the left side to hold the wheel in position. Put anti-seize or grease on the axle and then insert it from the right side (of the bike). To avoid damaging the thin-walled axle, tap it in gently and rotate it using the special tool from your Ducati tool kit. Once it is in, line up the holes in the axle with the holes in the axle clamps so that the through-holes allow screwdriver access to the compression valve adjusters.
The common mistake made here is to just tighten everything up at this point. Instead, here's the proper sequence to assure that the forks are aligned.
Temporally tighten-up the two RIGHT side axle clamp bolts so you can torque the axle nut.
Put on the (left side) 28mm axle nut and torque it (63Nm.)
Then torque the two LEFT side clamp bolts (19Nm.)
Now, put the brake calipers back on using the proper torque setting (43 Nm.)
Now, loosen the two RIGHT side clamp bolts.
Take the bike off the paddock stand, and bounce the suspension up and down till you are sure that the right side fork has moved to the proper (neutral) position along the axle. (It makes it easier to compress the suspension if you hold the front brake on when rocking the bike forward.)
Once this is done, torque the two RIGHT side clamp bolts to 19Nm, reconnect the speedometer cable, and you're done.