In my first hand experience the factory JZS161 engine ECU will throw an error without the speed sensor.
Personally I tried generating the 3 wire (R154 in my case) speed sensor and this caused a very low speed, speed cut, the only thing I can think of is that this was related to the traction control and lack of these speed inputs...
I'm not sure what you mean by "I've noticed that idle control is run though a speed sensor"... yes the speed sensor plays some part in the idle control, but in general not having a speed sensor will only have very slight effects on the idle. The fact the the engine has a "fly by wire" throttle doesn't really effect how the speed sensor effects the idle.
In other thoughts I suspect you will also have a number of error codes from the missing auto trans and the missing body ECU.... I was always planning to install an aftermarket engine ECU, but regardless I never managed to get the factory JZS161 or JZA80 VVTi auto engine ECU to run the engine to what felt like its true potential...(it felt like limp mode).
Cheers
Wilbo
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