I'm not going to get too heavy into throwing out random suggestions as to how to fix your tune. However, I am going to suggest one concrete thing. You state you have 6.1 injectors installed in the vehicle, so my question after looking at your injector data would be, why didn't you use the OEM 6.1 injector data that is available from many different OEM calibrations that have been posted both on the forums and the repository? I understand that not all of it translates directly over from different PCM OS table layouts vs your PCM table layout. But there's enough data there to get it damn close.
Your Inj PW vs Fuel Mass / Fuel Mass vs Inj PW tables are in some instances close'ish (with a few massive exceptions that I'll depict in this post). But your Inj PW offset data (which, again, isn't going to be a direct copy/paste affair) is off by an average of about 5% over the entire range in the 0 pressure column (the 6.1 calibrations lacking any sort of pressure definition in said table).
Let me show you what I mean with your fuel mass vs pw tables, and how far off they are from OEM defined calibration.
Here's the overall data comparison with the 0 point data being omitted (modified section being your data, stock being OEM supplied 6.1 injector data). Notice the 825% deviation from stock in the lowest PW row.
6.1_injector_data_1.JPG
Now, here's removing the lowest PW data point so we can get some better graph resolution to see how the rest of the data fairs. We still see that the lowest existing data point here shows a deviation of 160% from stock, and we start to see a little more definition in the remaining data points.
6.1_injector_data_2.JPG
Still, we can get even better resolution by removing the 160% deviation data point to see what the rest of the data looks like, and here's the result.
6.1_injector_data_3.JPG
So, I know there are some differences in the PW breakpoints and they don't always line up exactly. But they're not so far away from nominal that you can't see that there are some definite discrepancies. It would be my personal suggestion that you use the data that the OEM supplies for their 6.1 calibrations as closely as possible. There is an extra cell in the Mass vs PW / PW vs Mass tables. It's simple enough to create an extra data point (whether interpolated or extrapolated) at the end of your range, and using the same normalized factor (mg/ms - which is fuel mass divided by pulsewidth), select an arbitrary PW value to multiply that normalizer/multiplier by to get a Fuel Mass value for it. Conversely, you can simply make the extra cell value in your calibration identical to the last available cell value data in the 6.1 calibration, meaning your last 2 values (let's assume you actually use the OEM supplied data - in that case the PW value is 100, and mG value is 442.47 - so the last 2 cells would just repeat that).
As for the Inj PW Offset table, I'd just ensure that at least the 0 pressure row is identical to the data that is available in the 6.1 calibration. From there, it may take some experimentation while monitoring fuel trims during light throttle/vacuum scenarios to get the offset data closer in the vacuum sections of the Inj PW Offset table. Of course, having a control with VE would be nice to make that more easily achieved, but that will be quite difficult given you don't have a good control with your VE map (given the nature of your Frankenstein setup).
Start with accurate (or as close to accurate as you can get) injector data, and a lot of other issues you're dealing with may possibly disappear.
If I have missed a calibration that has tables more similar in nature to those in your calibration that also use 6.1 injectors from the factory (and that's where you derived your injector data from), let me know so I can update my information. But I don't believe there to be a calibration with tables like yours that used 6.1 injectors. So, interpolation and extrapolation will be key in getting at least the injector data portion of your tune ironed out.
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