i will try my best to answer some of your questions. there are people that have made professions by helping guys like you, but i'm a lifter. i love lifting as much you love running.
so here goes....
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Does this incompatability work on a muscle basis? i.e. If I do all my cardio using my lower half (given I generally run on my legs), but do my weight training on my upper half, will I get away with it, and benefit from both? That would suit me down to the ground, since it's my upper body I'm interested in bulking out, and I'm quite happy with my lower body.
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i believe that you should do strength training on all parts of your body. upper and lower. it is true w/ all of your long distant running your lower body might now increasing in mass as much as your upper body. however, doing strength training for your lower body will make your knees and chins less susceptible to injury. trust me i know this from personal experience. stronger leg muscles in general can only help your running.
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Alternatively, what if I were to seperate the cardio and strength training into different days? Or even different weeks? Say 10km run on Mon and Tues, then different setsor strength trianing on Wed, Thurs, Fri?
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doing each exercise on a different day is realisitic. you will have work with different loading parameters that best suited for your level of activity. do enough so you're not beaten up for your running the next day. read the following article to design a weight training regiment that is based on modern training principles:
http://www.mensfitness.com/fitness/41 .
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On a similar topic, I mentioned that I've always done cardio to burn calories, but now realise many see that as unnesessary. I'd be curious to know how many calories a set of reps of various exercises burns. Could anybody give me some examples?
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i never personally have believed that cardio is mandatory to burn calories at all. i lifted heavy for about 4 months and watching my diet, lost 30 lbs. this is with no cardio. i hate cardio. try lifting 5 sets of 5 or even 4 sets of 8 w/ only 1-2 min rest between sets. matter of fact here's a program that burns off the calories w/ nothing but weights:
http://www.mensfitness.com/fitness/44 .
and as for running. many people who lift also do HIIT (High Intensity Interval Training). i am sure you have heard of it.
good luck and hope that helps.
btw...when lifting do compound exercises. more muscles worked with less time involved. good luck.