Sorry to join the discussion late...  

What prompted you to take the thermostat housing off in the first place?  Was the car overheating?  Leaking fluid?  Check engine lights?

Zerex G-05 should be a safe coolant for the MINI, it is phosphate and nitrite free which is what is required for the new MINI.

If the thermostat housing was deteriorating, do you know if it is the original factory housing or do you know if it has been replaced? 

There has been issues with the original factory housing where the temp sensor in the housing would get corroded sending inaccurate readings to the computer triggering a check engine light.  This prompted several iterations of the housing and in some cases, an adapter is necessary to connect the new housing to the original harness.

ken

Two lines of thought here:
1. You have a head gasket leak (or cracked head) that allows oil to pass into the coolant. The oil pressure varies from 0 to 60 or so, while the water pressure varies from 0 to 16 psi. If this is the case, you could also have coolant in the oil, which is real bad for the bearings.

2. You did not flush out the old coolant properly. At the very least, you should have opened the heater valve to maximum heat and run the engine until it was hot, drained the system, let it cool enough that the fresh water going in would not crack the head, filled it with fresh water, run until hot and circulating thoroughly (at this point I like to just let the water hose run into the radiator slowly filling a little while the old comes out the bottom, but not so much as to end up with cold water going into the head), drained it, let it cool, and then add the coolant.  

In any case, if there are any residuals of corrosion in the system, after the first flush, but before the coolant, I recommend adding a radiator flush product (liquid preferred) and letting it run for the 15 or 20 minutes it will say on the package. Then an additional flush to get out all of the cleaning product before adding the coolant. This is a water pump that still has residue from the acid cleaning, probably with undisolved solid cleaner.


In any event, when all finished, you need to drive it until hot, let it cool, and check the level, as it will have tried to push the air out and pull in coolant. I always drill a 1/8" hole in the thermostat so that no air can get trapped in in on the paraffin (engine block) side.

Did you flush the whole system? What did you use as coolant? 

Update... NOT GOOD.  I replaced the thermostat housing. I bled the air out of the system.  Ran it for about 10 min.  Now the coolant turned greyish and cloudy.  It doesn't go away...Is it oil? If so, thoughts?

This is his first post in this thread. I dont see any mention of a beamer mini anywhere.

Well if thats the case , go to North american motoring.com they deal mostly with these bmw minis, i believe it has a lot of problems thats why they put up a site just to cater to these Bmw mini issues., 2 friends of mine owns these binis and they bring it to the mechanic more often than i open the hood of my classic.

Just for Tony, our (un-)Specialist.

See if you actually read the thread Tony instead of just mouthing off your bullS*** you would have seen right at the start where he tells us it's a 2010 MINI............

hmmm, i supposed your car is a BMW Mini ?? right? , because someone said it's a 7 year old car, i did my math 2017 - 7 = 2010. and issigonis's last production of mini was in the year 2000. so it can't be a classic mini., sorry , my advice is for classic mini not for Binis...i apologize for the confusion..

but there was never a mention that your car is a BMW, not even in your profile, and it's a 7 year old car??? I'm really confused.

HOAT coolants, as you are using are the most reliable and least troublesome in most conditions, as they tolerate more mixes. But they should be changed by 5 or 6 years max.

They really can't eat anything in the thermostat unless you have a poor ground to the engine causing excessive electrolitic discharges.

Rinse completely, clean everything, check grounds, and replace the coolant.

(one caveat: I once had someone try to save money buying the concentrate and adding his own water. When he went to buy distilled water, the sales guy sold him battery acid. Ended up with a hundred holes in the radiator.)

The pipe behind the engine goes to the water pump. again it's just an o ring seal at both ends 

You should not need to use a radiator flush agent for a 7-year old car. Additives may have gotten you into this mess. Have a look at the condition of the coolant (if there's any left) and where you have the thermostat housing apart. If the coolant looks clean and the passages around where the thermostat housing goes aren't calcified or rust coated, you don't need a flush agent.

You shouldn't need to drain the heater separately. Although it may not be self-draining through the block, it is one of the "pool" areas I wrote about. Most modern cars have coolant flowing continuously through the heater core and use air gates to regulate cabin temperature. Just make sure your heater controls are set to full heat. Each time you run it between flushes, once you have hot air coming into the cabin, you know that coolant has been circulated through the heater core. But remember, you need to continue running the motor (with coolant!) until the thermostat opens and the main rad heats up.

There is no drain for the heater element, the only way to dran it is to remove the coupler and pull the hose , but to me i wont pull it, i will just run a a regular garden hose for few minutes to glush the impurities and rust particles inside. And also tale the thermostat out and look if there are chunks of rust inside, use dremel to remove it.

The radiator has a very low hose with a coupler behind the bumper, Im good to go there.
Where might i look for the heater drain?  Anyone know where the plastic tube behind the motor goes? (it feels very loose)

Does your radiator have a drain ? If not good luck. If you really wanted to clean your cooling system thoroughly, get a radiator flush, pour it inside(not outside) the radiator then drive your car, i usually let it stay there for 3days before i flush it out and put fresh 50/50 coolant.dont be scared to use radiator flush, they were developed for a reason, and were tested million times before they sell them to the public. Be open minded, dont be like others i know.

Look up... Ooops

Typically, to flush an engine cooling system, you do it fully assembled. Drain and refill with plain water several times, running the engine each time to ensure the water gets pumped throughout the system, eliminating any pooled old coolant. If the car has a heater system valve (e.g. classic Minis), the valve needs to be open. If a thermostat is installed, typically the engine needs to be warmed up each time so that circulation includes the radiator. Be careful not to pour cold water into a hot engine.

So where does that plastic tube go behind the motor? Can i just flush it from the opening?  Im guessing the back 2 hoses go through the heater and can be flushed easily...

Acidic coolant from lack of service, or mixing of incompatable coolants could be any number of things. when removing housing just be careful when disconecting the rear tube be gentle and work it off.

Sorry for not clarifying...
I have a 2010 MINI Cooper S (R56 i believe).  Im hoping the other plastic tube that goes behind the motor is not compromised by whatever ate the plastic inside the thermostat housing.  Any ideas of what caused this problem??

I take it this is a MINI not a mini? The thermostat housings on the MINI is a known problem with defective seams and leaks, I would just replace the whole assembly and have done with it. Use the recommended coolant for the year of your car after giving the whole system a good flush out with plain water. 

You should identify which make and model of car you are taking about. It would help determine the problem (though it wouldn't help "Specialist" , who isn't one). 

"ZEREX^™ G-05^™ is the automaker approved original chemistry used in newer Ford & Daimler Chrysler automotive and diesel engines. Its Hybrid Organic Acid Technology (HOAT) chemistry combines the best of conventional and organic acid-based chemistry to provide the ultimate protection against rust and corrosion. ZEREX G-05 antifreeze/coolant uses the highest quality virgin ethylene glycol for freeze and boilover protection and a hybrid organic acid corrosion inhibitor package to protect your engines from liner pitting and corrosion. "

What does the manufacturer recommend for coolant?
Any additives thrown in?