If everything is not lined up properly, recheck your work. If it's been a while since you did so, this would be a good time to adjust the valves. Reinstall everything in reverse order of above. Restart the engine and let it idle for about 10 minutes. There may be some timing chain noise during this time until the tensioner piston gets pumped back up with oil pressure.
Test drive the car and check for any oil leaks.
If your engine had some timing chain noise before, it should be much quieter now. You might also want to change the oil and oil filter just in case some debris fell into the crankcase.