Hello mate, just some of my thoughts on the subject.
Definitely get off the treadmill and onto the roads and do some real running, it is very different and puts different stresses and strains on your body, especially the tendons.
Try and include some hills and cross country within your routes too,it strengthens the tendons in the ankles and knees and when you go through basic there is obviously lots of that lovely stuff.
Dont just run a mile and a half to train for your PFT. Run for a set time not a set distance. That way you're building your stamina and running further as you get fitter rather than running the same distance quicker and cutting the actual time that youre exercising down.
Interval training is the number one for improving your PFT mile and a half time. Run lets say 300 metres at 50% of your maximum effort then run 100m at 80-90% of your max. Then again 300m at 50% and again 100m at 80-90% and just repeat. If you dont have a track use lampost intervals and just run 4 lamposts at 50% to 1 lampost at 80-90% or similar. The interval is the rest part (50%). Do that for half an hour twice a week and you will start to fly!
Ive rabbited on enough now and probably embaressed myself but i get into these things and well...... dont forget your pressups( as many kinds as possible, experiment with different hand positions) and abs (dont just do situps! Use Crunches, twist situps, leg raises etc etc).
The number one upper body strength builder...pullups. Include them in your training.
If you want any more in depth help, email me. I am a Pti at 29 commando and have just scratched the surface here. Hope its of some use and i dont just sound like a complete co*k.
good luck.