I'm actually going to try and pay it forward and answer the questions.
Tuning VE with a histogram based on fuel trims only works in closed loop. The idea is (and its same for GM) the values in the VE table are an estimate of how much air mass is in the cylinder at the specific RPM and Pressure Ratio for that cell of the table. The ECU uses the value in that cell as the initial value of fuel to be added for that much air-mass to achieve stoich, about 14.7parts air per 1 part fuel... its actually allot easier if we think of 14.7 to 1 ratio as 100% of "perfect"... or just 1.00, anything greater than 1.0 is lean, anything less is rich. With the engine in closed loop, the ECU monitors the behavior of the front O2 sensors adding fuel when they stop cycling on the lean side, and subtracting fuel when they stop cycling on the rich side. The amount of fuel added in % is shown in the Short Term Fuel Trim for each bank... if the value in STFT persists, the ECU sort of "integrates" or stores the value in long term trims and at any point in time if you look at the sum of STFT and LTFT for each bank you know how much the ECU has had to add or subtract from what it started off with from your VE table cell values... as you build the histogram, you end up with a table of values + and - that can be used to "paste multiply %", etc, to the values in your VE bank tables... and essentially you can flash in the new tables to your ECU, and hopefully it won't have to add or subtract fuel when it is operating at the conditions of the adjusted cells. The purpose of turning PE off is that the ECU starts adding additional fuel when it goes into power enrichment, which completely throws off the process, at least on my NGC4 ECU, that's no longer closed loop... so if you go into PE while collecting data to correct your VE tables, the data you collect, if used to adjust your VE will just mess things up. To make matters worse, if you have PE turned off, and you, especially with BOOST go into very high mass values, no extra fuel, you are certainly operating in a lean condition under boost, which is a recipe for detonation, engine damage, and just a very costly day. Tuning VE using STFT and LTFT is only to be done lightly driving, no sudden acceleration AT ALL, you try to mildly let the engine run in as many pressure ratio and RPM states as possible, and usually you can't get to high or low pressure ratios or high or low RPMs, and you sort of spread the values from your VE histogram to fill in the empty cells to the perimeters of the data collected... I always err on the side of adding to the VE tables (making them richer in cells) than taking away... because it's simply safer to run with too much fuel than not enough.
The commanded air fuel ratio essentially comes from the values in the VE table. PE is an additional amount of fuel that is added when PE is activated by putting your foot in the throttle.
Stay out of the throttle, cruise mildly, make sure you are in closed loop. You should probably turn off DFCO, because that features shuts off all fuel when you are coasting or whenever you let your completely off the throttle and coast. You'll notice the Pressure Ratio goes to the top cells of the table, because when coasting the manifold air pressure is low compared to atmospheric. (Pressure ratio at any given instant in time is = manifold air pressure at that instant divided by barometric pressure at that instant.
I would recommend starting by reading one of the books by Greg Banish to get started...
https://a.co/d/5fwvnXN
