Reassemble Clutch & Brakes

1. Install the flywheel.
2. Clean the flywheel and pressure plate friction surface with thinner or acetone.
3. Position the clutch disk and pressure plate against the flywheel with the clutch held in place with an alignment tool such as old input shaft.
4. Make sure the clutch disk is installed properly. Make sure the marks you made on the pressure plate and the flywheel are matched up. Make sure the clutch disk is against the flywheel, then install the pressure plate.
5. Loosely start mounting the bolts in the flywheel, tighten them alternately back and forth across the plate to prevent distortion of the cover.
6. Loosely install all the mounting bolts.
7. Install the clutch release bearing if removed. 
8. Reinstall the engine.
9. Adjust the clutch pedal.