Adeeb Chowdhury

It is common practice to stack the doughnut type sensors and it works fine.  

Any of the base tunes provided are most likely *not* going to be the same values as a stock ecu.  My personal experience with Toyotas is that the OEM ecu is extremely aggressive on ignition advance and relies heavily on the knock detection system to keep the motor safe and pull timing.  Most often when switching to engine management I've found that all things being equal (boost levels, standard pump fuel, etc.) power is slightly lower on relatively stock engines once tuned and "safe".  It's going to take a lot of fiddling to get the knock thresholds right, as well as the detection frequency and gain levels right I find.  A 1jz should have 86mm bore and so use the 6 or 7khz narrow band unless the signals are all to high even with a gain of zero then go to the second order frequency of 13 or 14kHz and play with gain again to ideally get a clean run to redline with the vehicle not experiencing knock and maximum knock values in the 600-700 range.

if you do the timing light test with the set base timing window open while connected to the ECU then it forces it to that angle which can be more reliable than trying to set tables and trims.
If the ignition angle with a timing light matches the angle specified in the Ignition Angle runtime then it is the correct offset, do note that there can be some variance in timing marks on covers so you can check actual measured tdc against the cover marks if you are unsure.
You need to use a throttle stop yes to set an appropriate amount of air flow, then calibrate the TPS and then you can use ignition idle to move it around within a small range around that.

You will need to give us a log of the trigger error occurring, typically if a trigger error occurs near peak cyl pressure then you have ignition noise getting into the trigger signal. 
 
In modelled mode the fuel table represents volumetric efficiency, so will be a lot different to a traditional fuel table in many cases.  Typically numbers around 60% in the idle area and 100% near peak torque area.  You can likely just put 80% in the whole fuel table to get it running.  

Not really, the master fuel is a multiplier so will affect the size of the final numbers in the fuel table, the max value that the fuel table can take is 150, so if you for example had the master set too small you might start tuning at low rpm/load, and have values of say 100 in the fuel table, then when you get to higher loads you find your fuel table number is maxed out so you cant add any more fuel.  Conversely, if your master was set too big, then you could have very small numbers in the fuel table, which would affect the resolution of adjustment you have.  
If the values in the middle of the fuel table are around say 30-90, then the master is fine.

No, it should be the opposite, increasing the master increases the injector PW.  Set it to 5 to see if it improves the stumble or response issue, we dont care if the idle AFR is richer as that is not where your issue is. 
 
The master fuel setting is the overall fuel scaler.  The Fuel flow table is irrelevant, this is only used for fuel consumption calculation.   Adjust the master fuel until the engine runs then tune the individual cells in the fuel table to achieve the target AFR under all operating conditions.

You are really going to need the lambda working to be able to tune it, but my guess would be you dont have enough fuel, try increasing or decreasing master fuel to see if it improves in either direction.  

your ignition switch input is inactive and so it is cutting all spark and fuel, ignition switch needs to be active or the input turned off for the engine to run.
Also your MAP value doesn't move when cranking, was that log taken with all the spark plugs removed?