Given that he says that F11 and F12 were skipped because they didn't exist on the IBM keyboards at the time and given that he listed them starting from F10, it seems reasonable to assume they started assigning the keys from F10 working down, making F4 the next after F5.

Also unless things were different early on, the functions you're listing are the unmodified ones, not the functions you get when holding alt.

Yes. I regularly use F2 and F3. F1 help I cannot remember the last time I used it. I also get irritated by windows applications that do not use F3 for find next. I do not use F4 without a control or alt combo though...