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Been there and done that.

It is not likely you have another bad TB. What is likely is that there is corrosion, etc in the stupid round 10-pin connector which points toward the rear of the car and which has no rubber to protect the connections from the elements and the air stream around the engine...

As you may know the Throttle body /DME in the M52TU engine is extremely sensitive to changes in resistance, voltages, etc. A deterioration in the wiring is likely a cause of your issues.

you have a couple of options.
1. Spray de-oxit or something similar in the back of the connector - might or might not work
2. Replace with a used M52tu harness - might last for a while
3. Replace with a new harness - part# avail on RealOEM. Expensive and likely not avail.
4. Replace just the connector as outlined here:

There are people who have tried - with mixed success - to wire in an M54 Drive by wire pedal. Usually done as part of an upgrade from M52TU to M54. Not easy, and full of risk of add'l problems - Not recommended.
 

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Most of the time this issue was caused by the TB butterfly valve seized and doesn't move freely. Clean up the TB barrel around the valve should fix it.
OP has already replaced his TB once...So were both butterfly valves seized?
It's fine to clean the throttle body, I just wouldn't manually open and close the main vane. Treat it gingerly.
 

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10 years ago when my wife cracked the cylinder head and hydraulock the engine with coolant in cylinders.....The moisture from the coolant in engine corroded the TB aluminum barrel and locked up the butterfly.
Most of the time this issue was caused by the TB butterfly valve seized and doesn't move freely. Clean up the TB barrel around the valve should fix it.
Sapote a cracked cylinder head that leaks coolant into the intake and throttle body is pretty damn rare. Is that what made you say "Most of the time" TB Butterfly seized...?

OP should certainly clean his TB - very carefully without manually opening the vane. But I am willing to bet he has the much more common M52tu throttle body wiring issue.
 

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BMW (and many other manufacturers) strongly advise the use of "Stabilant 22" for applying to the connector pins, both male and female for such instances. It's fooking expensive, but if there's a connection issue with the pins and varying resistance is the root, the Stabilant usually fixes it.

FYI.
Thanks for this...It sounds a little like a commercial/professional grade De-Oxit. The first google search result on Stabilant 22 came from Boeing....

I think I am going to try it before I either replace harness (with another used harness) or replace pins as suggested above...

Here is a description of Stabilant 22: '

"...Its advantage lies not in making new contacts better, but in keeping contacts operating as if they were new, while making old contacts function perfectly despite the ravages of time and adverse environments...."
 

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I have bought used wiring harness, cut the 10 wires leading to 10-pin connector and am about to re-solder that into my existing harness. Similar to the @Effduration's 4th suggestion. Was practicing soldering during these few days... Any tips before I ruin the harness is appreciated.
I am about to go thru this myself. I have a complete spare harness for my '99 E39 528i with M52tu. Rather than cut and solder, I think I am going to replace the entire harness with the used one I bought. I will put "Stabilant 22" or DeOxit on all the connections of the 10-pin connector for the MDK (throttle body).

This is more work, but I would rather not cut two harnesses if I don't have to... I don't mind having to replace the harness because I need to do the cooling pipes under the intake manifold anyway, and with the intake off, replacing the harness is pretty easy.

If this doesn't work, I will cut and solder the connector on my original harness per:
 

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Fair enough...I wasn't intending to hijack the thread..although I think any discussion of testing the MDK would be less than complete without a mention of the 10-pin MDK connector which seems to be a common source of problems...at least as common as a failed MDK.
 

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Nareck, can I confirm what you have done?

You took a used M52tu harness cut off the 10-pin connector on the used harness and soldered into your original harness is that right?

This should work, but I worry the connections on the used harness are just as bad as the connections on your original harness....although it sounds like the errors you have now are different than what they were.
 

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What makes you think so?
Well I think the M52TU 10 pin throttle body connector is of a flawed design, exposing highly sensitive TB connectors to engine heat, air flow, and elements with little protections.

So, soldering in the connector from a used harness would be bringing all those same issues to your original harness.

I think I would prefer to solder in new wires and connectors. As noted here:
 
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