koracing

No, I think his problem was he had no aux outputs left so he had the tacho adapter connected to a coil drive, so you only get a very short pulse the length of your dwell setting.  If it is connected to an aux output that is set to the tacho function you have full control over the duty cycle and scaling.   I have never had any drama achieving a fully working tacho with one of these coil simulator type devices.
For me a $25 (or even the $100 8920) adapter is a no brainer, the hours it takes to pull the dash apart, modify it, reassemble, risk of breaking brittle plastic trim clips etc is a last resort. 
 

I can only imagine the frustration of having all lights green and still having it rough. lol
What exact model ECU? What exact year and model car? What exact make, model, and year engine? What green lights are you talking about? Do you have a copy of your tune you can attach? Do you have a datalog of the car running?

The high threshold is about 1.6V, low threshold is about 1.0V.  The DI pull-up if enabled is 4K7 to regulated 12V, there is a low drop schottky in series with the pull-up so consider it more like 11.7V pull-up.  I would expect it should work fine with almost any automotive hall sensor out there provided the sensor and ECU ground are at similar potential. 

The sensor on the trans is a hall effect sensor - so you would need to create a similar square wave output from the ecu - I'm not sure if any of the PWM outputs could do that natively or if you would need to add some other hardware.  
Without using the Link you can use something like the Dakota Digital SGI-100BT which has the ability to adjust an electronic speed signal.

It may help if you set your fuel pump output to turn on (Aux 7 output).  The circuit opening relay will turn the pump on while cranking or if it sees the start signal, but the ecu has to tell it to stay on after the starter disengages.

Toyota sells many of the plugs separately if you can get the part number off of the connector - usually starting with 90980-#####.  That said, what connector specifically are you seeing as faulty?  Did you correct the fuel pump output setting?

Your fan relay (assuming it matches up with generic bosch relay pin numbering like most relays) will have a ground trigger (pin 85) and a switched 12v trigger (pin 86).  You will want to source switched 12 to pin 86, and run the pin 85 to an output from the ecu.  Without knowing which exact model ecu you have (S13X? S15X? GTRX?) I can't help you determine which outputs you have available specifically.  
So Which ecu do you have?  If it's the S13 - then you have an 8 pin expansion connector with 4 ignition outpus on it (IGN 5, 6, 7, and 8) that can be used to drive the pin 85 on a relay to trigger it.
I don't know what a z's expansion loom is - have more information on that?

It would also possibly depend on if the logging screen is being watched while logging, or what you have displayed on the screen while logging.  I will use a blank page/tab so the logging connection is faster and more stable if I'm pc logging while driving.

I wouldn't worry about 370kpa too much as it's well over what you should need and you do have FP compensation anyway.  Maybe set up an alert of some kind if fuel pressure drops below a particular threshold.

I think the instructions were on their site and they listed some part numbers as "MAP sensors" and some as "Standard Pressure sensors" - but the calibration scales told me they are gauge vs. absolute when comparing them.  Their documentation could be better.

On one hand I agree the base maps as provided by Link are far from the best base calibrations I've used.  On the other hand, I've worked to develop my own base maps that gives customers a reason to choose me as their dealer and tuner.  If the base calibrations were good to go without much adjustment, people would tend to buy the ecus and possibly never seek out professional tuning help.  This could lead to very bad results and ultimately Link would be the likely target of any blame for a poor result.  By providing "startup only" tunes they force the end user to find a competent tuner - or to find these forums and seek help here - so that someone with more experience can get involved and help them go through all the necessary parameters.  This seems like the more conservative strategy and should - in the end - provide a better result.  Link gives out tuning aid free of charge here if you have specific questions to ask which is far more than most ecu manufacturers do.

The Atom does not have a built in MAP sensor - you would have to move up to the Monsoon for that.  I'd go to the Monsoon just for the greater number of inputs/outputs.

Xtreme understatement.

Yep, that seems to have fixed it.  Per usual, it's user error on my part.  =)

You'll want the ST205X ecu I'm fairly certain.  I can tell from the white EA1 connector attached to the side of the ecu in your pic that it is a later MR2 Gen 2 ecu with 3 rows of pins in that white connector (aka V2).  The MR2 Turbo gen 2 3SGTE ecus of the same era are -17380 and -17390.  Earlier MR2 Turbo ecus that would use the ST185X would be -17330, -17331, -17332 (aka V1).  These earlier ecus did not have the white EA1 connector attached to the ecu and it was only a 2 row connector (wrapped in foam).

You'll want the ST205X ecu I'm fairly certain.  I can tell from the white EA1 connector attached to the side of the ecu in your pic that it is a later MR2 Gen 2 ecu with 3 rows of pins in that white connector (aka V2).  The MR2 Turbo gen 2 3SGTE ecus of the same era are -17380 and -17390.  Earlier MR2 Turbo ecus that would use the ST185X would be -17330, -17331, -17332 (aka V1).  These earlier ecus did not have the white EA1 connector attached to the ecu and it was only a 2 row connector (wrapped in foam).

Can you take a photo of how you connected the wiring?
Under Lambda 1 in the Analog inputs you should select "Link CAN" if you have the AEM X-Series wideband coming in on CAN bus.

You'll want the ST205X ecu I'm fairly certain.  I can tell from the white EA1 connector attached to the side of the ecu in your pic that it is a later MR2 Gen 2 ecu with 3 rows of pins in that white connector (aka V2).  The MR2 Turbo gen 2 3SGTE ecus of the same era are -17380 and -17390.  Earlier MR2 Turbo ecus that would use the ST185X would be -17330, -17331, -17332 (aka V1).  These earlier ecus did not have the white EA1 connector attached to the ecu and it was only a 2 row connector (wrapped in foam).

Or you know, they could just build this feature into the start up settings, wouldnt be that difficult rather than wasting I/O on a fairly basic function. 
Stop Switch & Antitheft will disable ignition, which is not ideal. You want the motor to turn over with ignition, so if there is fuel in cylinder it will still fire, just injectors wont fire on top of that. 

I would assume because leaner mixtures can keep the catalyst hotter and so make it work better.  By intermittently going lean it can keep the cat temp up.

Other wideband options: 
14point7 Spartan3 with CAN
AEM X-Series wideband with CAN 30-0310 (Don't use AEM 30-4110 please.)
Link CAN Gauge, or Canchecked MFD15 gauge or BTI gauge are all options to monitor for relatively low cost.  An old laptop for $100-200 also works if you want that floating around in the car.
To take full advantage of the data gathering and advanced fuel model the Link is capable of I would add a fuel pressure sensor (of good quality) to your list as well since the link can do fuel pressure fail-safing and monitoring if you have this added into the fuel model strategy.  Good quality would be Honeywell, AEM stainless steel pressure sensors (stay away from the brass pressure sensors), Link sensors, etc.

Have you clicked on the "Read Notes First" button?  This will change to upgrade only after you have read the notes.  

show-off lol

Can you take trigger scope while cranking, and pc datalog of cranking, and post the tune, scope, and log here?

If you ever get the chance, plug one in while it's unmounted where you can see the flapper movement.  Then set the base position up and down and watch it move.  The spring loaded flapper nominally sits in a "center" position, and one side pin has to be grounded to get it to move toward fully open, and the opposite pin needs to be grounded to move toward fully closed.  Because two outputs are used to allow the full range of movement, they have to work in equal and opposite unison the way @Adamw describes.  

That said, I really wish there was a setting in the link to command fully closed when on boost.  It never drops below minimum duty cycle in the idle settings unfortunately.  You can make a 3D base position table to get close, but it's a feature I would like to see added.

Still broken as of now.