Before removing the flywheel, mark it to make realignment with the crankshaft easier. Usually the bolt pattern on the flywheel is such that the flywheel will only bolt on one way. Inspect the flywheel for damage. If the surface is flat, a sanding disc can be used to deglaze the surface. Heat from a slipping clutch causes cracks and warpage. A flywheel with this type of damage can be resurfaced by a machine shop. This is necessary to validate most clutch disc warranties.
Check the starter ring gear teeth to see that they are not damaged. Standard transmission flywheels have a pressed-fit ring gear. Sometimes a ring gear will be damaged due to starter motor problems.
Damaged ring gear teeth due to starter motor problems.
The damaged ring gear can be removed and replaced with a new one.
Use the correct quality screws on the flywheel and the clutch cover. These screws are usually shoulder screws (screws that do not have thread all the way to the top). When lock washers are used, they are usually serrated (especially on the flywheel).
When installing the flywheel, use the correct grade of screw (usually SAE Grade 8). Torque the screws to their correct specification. This is especially important on crankshafts that have a full round rear seal. The sealing area can be distorted if not evenly torqued.
Inspect the rear main engine seal and the front transmission seal for leaks while the flywheel is removed.