Cleaning it made it feel like it was moving slightly more freely. I didn't test the operation before cleaning but after cleaning the ICV moved nicely to both directions when electrified.
Next I did the mechanical set up of the ITBs. The S50 ITBs have a signle operating axle on top of the throttle bodies. This is operated via the throttle cable. The throttle bodies are split into pairs. Each pair is connected to the operating axle with a length-adjustable link:
The system is cleverly designed to have a progressive opening of the throttle flaps. With small openings the movement of the flaps in relation to the pedal movement is smaller and increases progressively when approaching the wide open -position. Factory workshop manual assumes that the adjustable screws for flaps closed -position are set at the factory and never tampered with after that. Mechanical synchronization of the throttle flaps is done by adjusting the length of the connecting links to have all the flaps close at the same time. This is tested by placing a strip of paper on each stopper screw and letting the throttle flaps close. When correctly set, it's not possible to easily remove any of the paper strips. Then the position of each throttle flap is measured at the wide open -position and the limit screw is adjusted by comparing the average value with the value given in workshop manual and adjusting accordingly.

Here's a link to the workshop manual:
https://workshop-manuals.com/bmw/3_series_e36/m3_s50_conver/2_repair_instructions/13__fuel_system_(s50)/54__throttle_and_operation/5_ra__throttle_body_basic_setting___exhaust_synchr onization_(s50_b30)/
Unfortunately my throttle bodies had lost the factory setting of these limit screws and they were all the way loose. So I began my set up with the information that on small throttle openings, all the throttle flaps should be open the same amount. I wedged the throttle lever into minimally open position and measured the opening gap of each throttle flap with a feeler gauge. Then I set them all to same value. After that I adjusted the fully closed -limit screws with the paper strip trick and checked that all the flaps close at the same time. Finally I set the fully open -position according to the workshop manual.
In addition to the mechanical synchronization there's a vacuum synchronization setting to ensure that all the cylinders get equal amount of air when idling. Each throttle body has a bypass channel around the throttle flap and an adjusting needle that limits the air going through this bypass channel. I carefully cleaned all the bypass channels and the adjusting needles and replaced the O-rings. I think these were the last seals in the engine that I hadn't replaced. Having a look at the needles before cleaning you can easily see which ones have been closed and which ones open:
While I was checking adjustments I double checked the cam timing. Having read M5X engine projects it's not uncommon to have have changes in the cam timing after the engine has been running. When originally adjusting the camp timing I was aiming for symmetrical opening of 1,0 mm of both valves at the TDC. I think I left the cams at 1,05 mm intake and 0,95 mm exhaust. However, now that the engine has been running the timing was 0,85 mm for intake and 0,9 mm for exhaust so there's a small change. Also, having read a bit more on cam timing, the symmetric lift for both cams doesn't seem to be the optimal setting. M5X engines seem to like slightly higher lift for intake cam at the TDC so I advanced the intake cam slightly and was satisfied with the values of 1,25 mm intake and 0,9 mm exhaust.
Meanwhile I got the INPA running on my laptop and had a look at the engine sensor values. There were to sensors that stood up. The TPS was giving a reading of 4,4 V at idle and 0,9 V at full throttle. Pazi88 confirmed that the values are opposite to what they should be. It's not surprising when you have closer look at the throttle bodies. Even though M52 and S50 have the same TPS sensor, the M52 throttle opens counter--clockwise when looking from the sensor while the S50 throttle opens clockwise. No wonder the idle was lost and the acceleration enrichment didn't work when the ecu thought the throttle was wide open when idling. Luckily the TPS is a basic potentiometer with a symmetric operation so switching the pins in the engine wire loom for the sensor operating voltage switched the operation of the sensor to desired.
The second sensor the I noticed was the intake temperature sensor. The ecu claimed the intake temperature to be 38 degrees celsius while the reality was around 15 degrees. While back I thought I checked the sensor to be same in both engines but that's just not true. I think I was fooled by the US M3 on the compatibility list..
S50 plenum is made of aluminum and has a threaded emboss for the sensor while the M52 plastic intake manifold has a smooth hole for the sensor with an o-ring and a retaining clip. I addition the sensors seem to have completely different scales. I removed the sensor connection from the M52 manifold, cut it up and turned it into an adapter piece in lathe:
Then I drilled the sensor hole in the plenum into bigger size, tapped it into 3/8" pipe thread and glued the adapter piece into it:
I'm sure I could have found a sensor with the correct thread and suitable scale but a stock part is always stock part and makes the maintenance easier when you don't need remember where each sensor comes from.
After the changes, the extremely high idle was dropped to more reasonable (but still a little high) level and the acceleration enrichment started to work:
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