Jon, the lowering is my biggest concern. I do not want to lower it at all and there are quite a few shenanigans that would be needed to avoid that with a kit.
There is certainly a change to the "feel" going from a solid axle to an IFS and I recognize that a lot of people don't like that. Different strokes and all. Using stock mustang 2 parts, I would agree with the concern about the cheap and low strength construction. There have been a lot of improvements in the last 30 years and the fundamental architecture of the system is actually very good.
I explicitly want to do something bigger and more radical with this truck than just build it stock. I did a full frame off restoration of a 69 mustang convertible (had the bodywork done by another guy, but did the rest myself), a stock rebuild then LS swap on a 78 Corvette, a full up California smog legal LS swap on my grandmother's 84 F150, built a 14 second crew cab long bed duramax (with a buddy), and more smaller projects than I care to think about at the moment. I fully recognize the amount of time and effort that will go into a project like this, but I specfically want to do somethig bigger and better than what I have done before.
In an ideal world, I would do a full frame swap to a GMT800 with an LQ9, 6L80, and NP246. I just don't have the space and tooling for that now and don't expect to anytime soon. The level of effort needed to narrow the front end on that is non-trivial and I don't like the exposed tires look from leaving it at full width.
I do appreciate the feedback and perspective. I am exploring a lot of options right now, trying to plan out the long term project before jumping in and regretting an early decision. One thing that I do specifically want is to be able to do things in chunks and drive it in the intermediate states.