There are two kinds of motorcycle engine restoration: cosmetic and mechanical. To completely restore an engine is to do both. Many people have the skills to cosmetically restore a motorcycle engine, but fewer have the skill to rebuild one. Before you attempt to rebuild an engine, take stock of your patience, time, tools and budget. If you're committed, you can do it, but know what you're getting into.
Conceptualise the process. It's important you understand what "restoring a motorcycle engine" means. Motorcycle engines rub metal against metal in places. Motor oil keeps them from tearing apart immediately, but they wear. Gaskets help seal engines together. They wear out. These are the two functional things you're doing when you rebuild an engine: returning worn parts to their previous form and resealing gaskets. And you can make it look great in the process.
Lay out a clear plan and be decisive and organised. Before you even start, know what all the key components of your engine cost, where you can buy them --- new or used --- and what a machinist charges per hour. Find a machinist who specialises in motorcycles and knows your make and model. Know which tools you need and estimate a time line. Like any complex project, planning and organisation is essential. Check off these items and the "Things You'll Need" and then decide whether you want to continue.
Decide whether you're going to rebuild the top end of your motorcycle engine (cylinder, rings, valves, valve springs, camshaft and the rest of the valve train) or the bottom end (crankshaft, bearings, rods) or both. Top ends need rebuilding more often. So if it's a bike you've owned and there's no evidence of problems with the crank, consider opting for a top-end rebuild only. If it's an old motorcycle you pulled out of a barn and you're unsure of the condition, you may as well do it all while you have the engine on the workbench.
Disassemble the engine. Thoroughly drain the motor oil. Remove the engine from the frame and place it on your motor stand. Disassemble as described in your shop manual. As you remove parts, carefully clean, inspect and label them and then store them so they won't get lost or mixed up. Consider taking photographs as you go.
Replace or restore bearing parts. The easiest way to address most bearing points is to replace them. Carefully inspect all internal bearings. If you have any doubt about their functionality, replace them. Some bearings can be cleaned an relubricated. But once you're going through the trouble of opening the engine, you don't want to miss a part that needs to be replaced. Other bearing parts may have to be machined. For example, you may want to have cylinders resurfaced with a hone or have the camshaft welded and reground. Inspect and measure for wear. If it can't be replaced, take it to your machinist with the specs.
Reassemble the engine. After you've replaced or renewed all the worn parts such as bearings, piston ring, camshaft, valve springs, valve tappets, etc., it's time to reassemble the engine. When you reassemble, use a new gasket kit. Use assembly lube and gradually tighten things to factory torque specifications with a torque wrench. Do not over-tighten.
Cosmetically restore the engine. If you go through the trouble of mechanically restoring a motorcycle engine, you may as well complete the smaller task of cosmetic restoration. A lot can be accomplished by buffing aluminium cases or painting components. Consider media blasting the exterior, but be careful you don't remove metal from machined surfaces that contact one another.
Every engine has idiosyncrasies you may not learn about in a shop manual. Look to online forums specific to your motorcycle engine for experience and advice.
If you do only a cosmetic restoration and use media blasting, be careful not to get any media (sand, shells, glass-bead, etc.) inside the engine.