Chad Waterbury's PLP supplemental training for the pushup/situps, with some hill/flat/prowler sprints to build cardiovascular endurance. As for the run, to me it seems like there are people who are born with that part being really easy, others who are born for it to be a death race. For example, my first ever PT test, I maxed pushups and situps, but ran a 15 minute 2 mile.
For that, you'll probably just have to do some damn running. sucks, I know. maybe you should just go to PT, even if you do max the test.