When the engine is at top dead center, the keyway on the crankshaft will face engine vertical (to say, it points upward in the direction the engine goes), and the notch in the reluctor wheel of the crank gear will align with the notch on the front cover.
The camshaft when at TDC will show the mark on the front cam cap through the hole in the camshaft gear spoke.
See pictures attached:
Pay no attention to the "reference mark" notations on the cam diagram, that is only if you are reusing the same timing belt on reassembly.
The oil pump and water pump sprockets do not need to be timed, just the set the crank as pictured, verify you can see the cam mark through the gear spoke hole, and you are all set.
If you have any questions let me know, if you are all set and satisfied, please remember to click Accept to credit my time.
Okay, sounds like you still have a air pocket in your cooling system.
This engine is kind of a pain to get the air out of the system. I have a fancy bucket that seals to the radiator to effectively raise the water level to get air out. For one time use this isn't really necessary for you though.
Support the front of the vehicle at least 6 inches or so in the air with ramps or jacks etc. Remove the radiator cap and let it sit for several minutes with the vehicle off.
Fill the radiator up and start the vehicle with the cap off.
Standing in front of the vehicle, very slowly push the long upper radiator hose downward at its center. This is where the majority of the air gets trapped. As you push it down you will see either air bubbles escaping at the radiator neck, or the water level dropping. Continue to do this while adding fluid until the level does not drop anymore.
Reinstall the radiator cap.
Place a medium weighted object (I've used a half filled coolant jug in an emergency) over the upper radiator hose to weight it down.
Go inside the car and make sure your heat is turned to full hot, monitoring your coolant temperature gauge all the while, increase the throttle to 2000-2500 rpm in 30 second bursts. You should feel heat begin to come through the vents. If the heat goes away when you let off the gas, you need to keep doing it. When the heat stays after you let it idle, the air is out of the heater core.
Shut the car off and let it cool, then check the level at radiator cap and top off as necessary. Fill the overflow jug to just over the full mark as you will still have small amounts of air in there to take out.
Let me know how that goes, it should take care of you.
Assuming you did not disconnect them and they were working fine before the waterpump job, there is likely an air pocket around the sensor. It would have to be extremely hot for air to trigger the fan switch.
Get all the air out of there and I think you'll find everything is OK. Also be aware the fans (unless AC is on) take a long time to come on when running hot even in hot-weather conditions. In cold weather conditions even longer.
Great, I'm glad I was able to help.
If you need anything in the future, feel free to request me if you wish.
Have a great night!
I do a little, unfortunately Chevrolet is one of the few categories I am not listed in on this site (there is quite a waiting list to get in there apparently).
If it's something really quick you can I might be able to help you out here, if it is a full question I have to refer you to the Chevy guys though.
For future reference if you need me, I can help you with any other GM group product, Honda, Toyota/Lexus, any Chrysler group product, VW and Volvo, as well as any non-categoried cars (Mitsubishi, Mazda, Scion etc).
Good luck with your Malibu!