Some of these don't seem very well calibrated for 'minimum necessary to maintain a reasonable quality of life'.
Programming: Most people don't program at all, and do fine, so this might not be a useful category in the first place. 'Computer interaction' would be better, and level 1 might be something like the ability to use reasonably-user-friendly web-based email or the ability to write, save, and retrieve an essay in a word processing program. If we want to talk about actual programming, though, level 1 might be something like understanding what variables are, or that computers 'think' in a purely procedural way (that there is no ghost in the machine).
Math: I agree with atucker that basic arithmetic is appropriate for level 1, though I'd add 'ability to parse simple word problems' to it.
Endurance: I don't run. At all. This has approximately never been an issue, and doesn't affect my quality of life in any way that I can detect. Level 1 for endurance should probably be something more along the lines of being able to walk a few miles (2, maybe 3) on flat ground without becoming winded - this seems about in keeping with what someone would need to do in the course of shopping at a large store.
Empiricism: Again your suggestion seems too advanced for a 'minimum necessary' level. I'd suggest something more along the lines of being able to notice intrinsically flawed arguments or arguments where the arguer is obviously biased.
Perhaps we should refine "minimum necessary to maintain reasonable quality of life" to something like "minimum necessary to maintain reasonable quality of life, given that the area is relevant".
By way of analogy, I don't own a car. The minimum necessary skill in driving to maintain reasonable quality of life is absolutely nothing for me. But for many, driving a car is necessary; for them, the minimum necessary skill is being able to remain within the lines, use indicators, park and three point turn, etc. Pass the driving test, in other ...
I just got this random idea that people who want to become better at life could benefit from a common scale of "leveling". No, I don't mean vague Lesswrongey things like "changing your mind". I mean a set of concrete criteria like "you qualify for level 2 if you can do 5 pull-ups, have solved 30 Project Euler problems, and did 10 cold approaches". Obviously there would be separate ladders for different character classes, but not too many. Also obviously, my example was a bit too high for level 2. So I guess I really want to ask some meta questions here:
1) Do you think agreeing on a common leveling scale would be a good thing for a substantial subset of LW users? Would you feel good about leveling up and telling other people about it on LW?
2) Is there some good way to determine leveling criteria that are neither too high nor too low? Maybe make an intermediate scale of "experience points"?