1: The only thing I can think of is, your lambda overlay settings haven't been adjusted. Go to Options > Settings > Lambda Overlay and post a screenshot of that popup window. On my FP Manager, I show your fueling dead on at 0% from 4500 to 6000 RPMs. So I am pretty sure your settings haven't been adjusted to suite your target AFR.
FN2WOTScreenshot.JPG
2: With using speed density, there is no need to have it dip into the 12.14. Even using AFM there is no need for it to dip to 12.14, 12.46 across those columns is sufficient to transition the ECU into open loop mode. These don't decide the AFR, they just tell the ECU to transition into open loop. You then tune your fuel tables as you have where the fueling is good up top. You certainly don't have to change the settings, but the more you get in the habit of making this linear, the better your overall tuning strategy will be. You will need to tune each cam angle individually as you have on the low cam it looks like. Then tune the high cam in the same manner. Another issue I see is you don't have "MAP to determine WOT" checked under closed loop. This should be checked to ensure the WOT fueling is commanded when the MAP pressure falls into the determined range.
2.1: Another thing I noticed is your car never engaged into VTEC throughout the pull. Looking through your file, you have VTEC minimum engagement set at 124mph, did you want this set so high for a reason? For this reason, your car is never transitioning onto the high cam at all. I would be happy to help you with cam angle mapping. Without a dyno, you essentially use your fuel tables to determine the best cam angle mapping. I can help you read that as well if you would like. But running the RPMs too high without engaging into VTEC can cause harm to the engine, so be careful there.
3: If you tune on the AFM, I don't know 100% if your commanded AFR will be the same. I always set the values to 12.46 whether I am tuning the AFM or speed density, because all I want is the ECU to transition into open loop, then I make the AFR what I want either AFM or fuel tables for MAP based tuning. I would imagine it is the same, but I don't know for sure. For the time being, don't worry about changing the WOT tables for the high cam.
4: To tune speed density you should disable the AFM by unchecking the box for "AFM enabled", leaving the speed density box checked. It still makes the air flow meter to act as the intake temp sensor. SO don't remove the air flow meter, but uncheck the box for it. A lot of this depends on your modification list, what is the modification list on this car? If it is stock, you are probably best to run on the MAF sensor, intake and other bolt ons generally like to be tuned on speed density. Don't disable the AFM and set the minimum pressure to 700mbar, then it will cause an issue because it won't have a reading to go by. Leave the pressure set to 0, then choose whether you want to run the AFM or speed density. If you leave both boxes checked, and set the minimum pressure to 700mbar, then it will run the AFM until it sees the 700mbar and then use the speed density tables. Technically you would be running a hybrid tuning, which I have had no experience with either. Some people have, but I can't shed any light on that unfortunately.