Thats the sensor for the VVT Tensioner, really should be plugged in, although if you are running Emerald then only they know what needs to be plugged in or not.
I would entirely re-pipe the intercooler, same diameter pipe throughout will aid in air flow.
The MAP sensor should definitely be on the pipe that runs up to the TB, but again, Emerald may not need it as the early engines didn't have em anyways.
And yes, Ess_Three is correct in saying that RHS mounted TB's were all DBW from factory, not sure if Emerald sell the TB's with there kit like Qpeng do