Difference between S4 Auto and Manual trans Thermostat Housing
 

I need to replace the thermostat housing on my 88 FC, but it was originally an auto that has been swapped to manual trans at some point. I don't know if the engine and trans were swapped or just the trans, and apparently the thermostat housing is different between the two engines. I can't spot an noticeable differences between the two housings from pictures though, how would I determine which one I have? Or are they both the same?

There is no difference that I am aware of. Are you talking about the thermostat neck where the hose attaches to or the whole waterpump housing that bolts to the block?

Just the thermostat neck where the hose attaches

there is no difference as it is the same part...on the same engine.
The only thing that makes the cars (Manual and automatic) differ are the transmissions..not the engine parts.
well..not exactly true..some shifter stuff ,pedals or no pedals..and a vacuum thingie near the Air flow meter.(if you really wanna get technical!..haha!)

Thank you, was really confused to see what appeared to be the same part being sold as separate things for very different prices

On turbo and automatic cars, there is a water temp thermoswitch mounted in the t-stat housing for the auxiliary fans. The more expensive one probably includes the sensor or at least the threaded hole. They mount interchangeably, so you can use either.

There are Differences in the Engine parts IF the engine is an S4 Or an S5 though.
The difference in your case and your part would be the Thermostat neck and waterpump/housing.
The Neck on an S4 has 2 bolts to hold it to the waterpump housing.,usually made of aluminum.
The Neck on an S5 is a 3 bolt affair and is made of plastic.

Again if you wanna get further into this,the pumps differ by bolt placement(8 bolts vs 9 bolts) onto the housing but the Housing bolts onto the engine with no difference.
The fan is 8 blade on a S4 and 10 on a S5.The bore is different to place and mount onto the pump shaft so you by rights can't use the one to replace another series..BUT it is doable..(so that is why I stated that.)

I actually notice the threaded hole on the auto one now that you mention it, but that one is actually the cheaper of the two so that's what I'll go with

/\..and that thermoneck is an S4 neck.

yes, there are two. the turbo and a/t have a threaded hole for the auxiliary fan switch. the m/t NA neck has the casting, but its not drilled or threaded.