Adamw

The cam position would be able to go to "-10" instead of stopping at zero, the ecu will report errors and disable cam control if it goes more than a couple of degrees below zero.  

The wrx sensors look identical to that.  They are pinned:
5V Gnd TP Sub 5V Gnd TP Mian.   Im pretty sure the pin numbers are printed on the back of the plug near the wires.  

This is how normalised mode works. 
With normalised mode the ecu is comparing the noise level of the current combustion event to the previous few "learnt" combustion events.  If you are operating under reasonably stable conditions then suddenly increase load or RPM, then the first few combustion events at that new higher load will now be generating more noise than the previous events it is comparing to.  So to account for this, when there is a sudden change in load or RPM (this is determined by the RPM/MAP/TPS delta level settings, then the threshold is increased by the "Threshold gain" for the number of cycles set in "Delta hold".   
With normalised mode you would usually have a "flat" threshold table, and the threshold should only need to step up for a short time when there is a significant change in load or RPM.  You should not need to increase threshold with RPM or boost like your threshold table is, this suggests something is not right in the setup or possibly mechanical.  I notice you have a 2.5L whereas our car was a 2.0 so possibly the knock frequency is not ideal.  You could try it at 6,7 and say 13Khz to see if the noise levels look less erratic.  Your ignition advance is quite low so I doubt there is knock, but it is a little odd that your cyl 4 knock level is mostly the one that is erratic.  
A quirk I found in our subaru was the sharp click from the AC clutch turning on/off in auto mode would cause a spike in knock level, I got around this by disabling knock for a few tenths of a second before the clutch switched on of off.  I see that has caused 1 spike in your log but it is not your main issue, just something to keep in mind if you start seeing random spikes or retard.  

For the trigger scope capture you need to go to >ECU controls>Trigger Scope, then hit the capture button, once the screen has a waveform showing on the screen then click save.  Do one at idle and one with a free rev to about 5000.  

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.  

I was in the middle of a reply when Vaughan beat me to it.  So here is mine anyhow:
Are you capable of basic wiring/crimping yourself?  Link do offer a variety of CAN cables that could be used, but in this case since neither the keypad or CAN lambda has a built-in termination resistor I think it would be nicer to build your own bus.
Schematically we want to achieve something like this:

 
In practice there are several different ways to achieve this. One option is to arrange like a daisy chain, provided it does not need to be waterproof you can often crimp two wires into a single connector pin so a splice is not needed.  Something like this (not shown but CAN H & L would be twisted):

 
Using Link accessories would end up something like below, so possibly more complicated and expensive than it needs to be:

Your MAP sensor isnt working in the log so it has about 300% more fuel dumping in than it normally would, so start by fixing that to see if it helps.  You can test the ignition outputs by pulling the spark plugs out so you can see them, then use the ignition test function to test spark each output.  

If you have a plug-in ecu the hardware is already built-in and the hold power is already set up and working in the base map, you dont need to do anything.

From memory the gain and update rate table examples given by me above are from my Evo road car (pretty much dead stock evo 7) the lambda probe is very close to the turbine outlet probably at the most 500mm from the exhaust port, in this car I have the reactivation delay set to 3 samples.  In our WRX11 test car which also has the probe right after the turbine - but has much longer manifold primaries etc (probably more like 1500mm from port to probe) I have reactivation delay set to 5 samples.  The update rate table is similar in both cars, the subaru could actually do with less than 1Hz at idle as it takes about 3 secs to respond to a change of PW but 1Hz is currently the lowest it can do. 
So what this means is in my evo with the reactivation delay set to 3 samples, if CLL was temporarily disabled due to over-run fuel cut or similar around idle where my update rate is 1Hz (1 sample per second), then CLL would be re-enabled 3 secs later.  To give an example at the other end of the table, if I hit the RPM limit at 7000RPM where my update rate was 10Hz, then CLL would be disabled for only 0.3s.    

You can just put zeros in your 3D trim limit tables where you dont want CLL to operate.  
Not possible as the LTFT table uses a GP table which has a max cell count of 16 x 11, whereas the main fuel table cell count is 22 x 20.  If your Fuel table is 16 x 11 or less then you can use the import/export tool to copy it to the LTFT to get the same axes.

The most important one I see in the list that may affect you is to check the base timing after updating.  There was a change in 6.20 that moved the trigger offset by 1 tooth with the trigger some missing tooth trigger modes.  

Assuming the ecu has already been unlocked, then also check the antitheft runtime, the ecu will cut fuel and spark if the antitheft conditions are not satisfied.

It is not a set up issue in realdash or the ECU, you have the wrong device that will not work with any aftermarket ecu I know of, it "talks" only in the dedicated realdash protocol, the format of the message is not user programmable like the recommended wican or seedstudio CAN device.

You can vary the target with APS as you have set up.  Set up the control so that it only moves into stage 2 when you are somewhere close to the minimum achievable "spring pressure boost".  The lowest value anywhere in the target table should also be the same "minimum achievable spring pressure boost".  In stage 2 the duty cycle will still mostly be coming from the wastegate DC table just like it did in openloop mode but with corrections added depending on how far off target you are. 
  
In stage 3 the actual DC value applied to the wastegate comes from "Base DC"  + Proportional correction + Integral correction.  If the base DC mode is set to "Stages 2-3" then the "Base DC" part is coming directly from the base DC table.  If set to "Stage 2 only" then the "Base DC" part is fixed at the last base DC that was being commanded from the table when you left stage 2. 
I would suggest base DC mode "Stages 2-3" based on the shape of your base DC table.  You have a big change in your base DC table between 5&6000RPM so likely closed loop will need to do less work with the variable base dc coming from the table through the whole rev range. 
I dont think I have ever needed to use the "Stage 2" base DC mode but I suspect there are applications where there is some other factor involved that causes the DC required to reach target quite variable, but once you are on target the control requires less variation. 

This is how normalised mode works. 
With normalised mode the ecu is comparing the noise level of the current combustion event to the previous few "learnt" combustion events.  If you are operating under reasonably stable conditions then suddenly increase load or RPM, then the first few combustion events at that new higher load will now be generating more noise than the previous events it is comparing to.  So to account for this, when there is a sudden change in load or RPM (this is determined by the RPM/MAP/TPS delta level settings, then the threshold is increased by the "Threshold gain" for the number of cycles set in "Delta hold".   
With normalised mode you would usually have a "flat" threshold table, and the threshold should only need to step up for a short time when there is a significant change in load or RPM.  You should not need to increase threshold with RPM or boost like your threshold table is, this suggests something is not right in the setup or possibly mechanical.  I notice you have a 2.5L whereas our car was a 2.0 so possibly the knock frequency is not ideal.  You could try it at 6,7 and say 13Khz to see if the noise levels look less erratic.  Your ignition advance is quite low so I doubt there is knock, but it is a little odd that your cyl 4 knock level is mostly the one that is erratic.  
A quirk I found in our subaru was the sharp click from the AC clutch turning on/off in auto mode would cause a spike in knock level, I got around this by disabling knock for a few tenths of a second before the clutch switched on of off.  I see that has caused 1 spike in your log but it is not your main issue, just something to keep in mind if you start seeing random spikes or retard.  

The easiest would be with an expansion loom which has 5V, Sensor Gnd, AN Volt and AN temp inputs all in the one bundle. 
If you want to make do with existing wiring, then you could splice into 5V and ground at the TPS sensor, connect the MAP signal to AN Volt 2 in the airflow meter plug and the temp signal to old fuel temp sensor wire which I think is in the regulator.  

Have put a task in for this, not sure when it will be done.

Yes, for either of the 24T ones, I would grind a tooth off to make it 24-1.  The missing tooth gives faster sync and means the position of the cam sensor is not critical.  The 60-2 would be fine also, but it is quite big at 200mm dia.  The crank sensor we sell is a VR type from a ford focus I think, they work well with the tooth size on any of our wheels.  
If you want something more specific, I have various 3D models I can generate a custom size dxf that you could get laser cut locally.  

Your pic hasnt worked, but yes that all sounds ok.  Another option for the IAT is to wire to the MAF plug which is already in the engine bay with AN Temp 2 and a ground in it.  

There appear to be a few variations but it looks like the security light is controlled by pin 39 in the connector at the back of the cluster.  It is a brown/red wire in this diagram.  This would probably be the easiest place to disconnect as the other end can go to either the BCM or keyless entry module depending on options. 

There appear to be a few variations but it looks like the security light is controlled by pin 39 in the connector at the back of the cluster.  It is a brown/red wire in this diagram.  This would probably be the easiest place to disconnect as the other end can go to either the BCM or keyless entry module depending on options. 

The 2012-2014 models arent yet fully supported as I haven't been able to find a car locally to test.   CEL and airconditioning in some regions wont currently work in these cars.  I have been working remotely with a couple of US dealers when they have access to this year model but I haven't yet been able to figure it out.  So this will likely be fixed with a future update.  The security/immobiliser lamp doesnt work in the key start models that have the separate immobiliser, this is common with any aftermarket ecu in these cars.  The factory ecu and immobiliser ECU has an encrypted serial coms and they need to be "paired" with a dealer level tool.  The lamp could be disabled by pulling a wire out of the plug at the back of the cluster.  Hill assist will likely just be the missing clutch switch.  You can try assigning the clutch switch function to a math block and leave the equation empty, if that doesnt work, try 1 as the equation.    

This one should match:

To make it easy to get started on the forum each user gets a small storage allowance to allow them to attach log files, tune files and pictures to their post.  When you have used up that allowance and try to attach a file you will get an error message stating your file is too large to upload.  The way forward is to upload the file to an online drive service and use a share link to the file.  Google Drive and Onedrive are probably the most common free options in western countries so I have done a quick guide on those two here.  
There are many other options such as Dropbox, iCloud, WeTransfer, etc that usually follow a similar process.
How to share a file using Google Drive and Onedrive.mp4