To properly rebuild an engine, you must first remove it from the vehicle, then disassemble and diagnose it. Ideally you should place your engine on an engine stand. This affords you the best access to the engine components. Follow the manufacturer's directions for using the stand with your particular engine. Remove the flywheel or flexplate before installing the engine to the stand.
Now that you have the engine on a stand, and assuming that you have drained the oil and coolant from the engine, it's time to strip it of all but the necessary components. Before you start disassembling the engine, you may want to take a moment to draw some pictures, or fabricate some labels or containers to mark the locations of various components and the bolts and/or studs which fasten them. Modern day engines use a lot of little brackets and clips which hold wiring harnesses and such, and these holders are often mounted on studs and/or bolts that can be easily mixed up. The manufacturer spent a lot of time and money designing your vehicle, and they wouldn't have wasted any of it by haphazardly placing brackets, clips or fasteners on the vehicle. If it's present when you disassemble it, put it back when you assemble, you will regret not remembering that little bracket which holds a wire harness out of the path of a rotating part.
You should begin by unbolting any accessories still attached to the engine, such as the water pump, power steering pump, alternator, etc. Then, unfasten any manifolds (intake or exhaust) which were not removed during the engine removal procedure. Finally, remove any covers remaining on the engine such as the rocker arm, front or timing cover and oil pan. Some front covers may require the vibration damper and/or crank pulley to be removed beforehand. The idea is to reduce the engine to the bare necessities (cylinder head, valve train, engine block, crankshaft, pistons and connecting rods), plus any other "in block" components such as oil pump, balance shafts and auxiliary shafts.
Finally, remove the cylinder head from the engine block and carefully place on a bench. Disassembly instructions for each component follow later in this section.