You must first disassemble the powerhead and remove it from the leg. Take a LOT od digital pictures at each step because you may forget something by the time you reassemble. Then take the block to a good auto machine shop and let them tell you how far the bad cylinder needs to be bored. Standard over bores are: .010, .020,, .030, and .040. I do not like to go .040 because it leaves the cylinder walls too thin. Order a standard overbore piston to match what the block is bored. If the other two cylinders are good, only the affected one need be bored. The added cubic inch (partial) is so little that the engine will never notice it.
It is not possible to bore out all cylinders and increase displacement. Even going .030 on all three yields less than one cubic inch. You can increase power slightly by porting the cylinders but if you have never done it, stay away. If you want more power bolt a 120 or a 125 block onto your leg. However, given the cost and fuss, you would be better off buying a used running 125.
almost no special tools are needed to rebuild. A harmonic puller to remove the flywheel and both a foot pound and inch pound torque wrench are necessary. Expect to spend about 5 hours disassembling and a bit more with reassembly. It is more than likely that you will twist off a couple of bolts and they will need to be drilled and re-tapped. The machine shop can do this for you but if you are real careful use some penetrating oil and heat, and are lucky, you may not break any.
If you do decide to rebuild, come back and the guys will certainly provide more detailed help.