I drained all the coolent i could from the engine drain plug (under middle of spark plugs)... Now it's raining outside... It was full of water (no coolent) because I was cleaning it out... Is it ok to let my car sit for a night with no coolent in it?

 

Yeah. Its nowhere near freezing here

 

One more question... With the water in the system, I ran it for a couple of days (with the heater on all the time). I drained after a few days, it was not crystal clear, it was dark-brownish clear. So I rinsed the system out again till the water that came out was clear. Then filled it back up and ran it for some more days. Drained, still brownish clear... I see no sediments or particles of rust (then again, I never took off the bottom hose)... What's wrong?

 

the rainwater rusted the system. Same thing happens to brake rotors after heavy rain - a light coating of powdery rust.

You won't see large flakes, but you'll want to flush your rad then fill with coolant.

 

ok! rain stopped and i went ahead and popped on the new thermostat and gasket and now it's filled up with coolent! hopefully everything will be just fine

 

i ran some cleaner from advance through mine to clean out the deposits, etc.

 

like I said, FLUSH THE RAD, then fill with coolant. Don't just drown the rust in coolant and pretend it's gone.