You sound about where I am. My lower body is awesome, because I played soccer and focused on leg machines. But I've got a pretty pathetic upper body. Even after two years of strength training focused on increasing my upper body, I found it was tough to increase my max weight in those areas. But I wasn't putting 100% effort into it, I admit.
3) My goals are oriented mainly towards increasing my abilities, not making changes to my body (though obviously that's a side effect). My biggest issues as I see them right now are a complete lack of upper-body strength (for stuff like climbing, say), and pretty terrible endurance when it comes to anything, but especially things like running/bicycling. I end up out of breath and in pain after a few seconds (running) or a couple minutes (cycling). I want to change that.
Muscle endurance is one thing. You can increase that by low weight, hi-rep exercises. Cardio, however, is a different story. When it comes to cardio I prefer straight running, mostly because I prefer that kind of impact on my ankles than bounding on a treadmill. I'm sure someone will disagree with this, but weight rooms are generally not the place to go if you really wanna work on your cardio. Swimming is a great cardio builder....and as long as you have a pool, you might as well bone up on your swimming. (In case you fall into a river after a carp attack.)
There seem to be a decent variety of cardio and weight machines available, so I guess right now the key is picking which ones to use, and figuring out how much weight/repetitions to do on the weight machines.
One of the trainers/staff in the weight room should be able to at least give you a general idea of the sets you need to do...if they don't just straight up build you a workout plan right there. I recall the formula (which I'm not advising you to follow) was something like...
Find a weight you can do only three reps of before you're exhausted.
That's your max.
Subtract 25% of your max weight, and do that 9 times. That's a power set.
Subtract 35% and do two sets of 10 reps. That's the median.
Subtract 50% and do two to three sets of 20 reps. That's a toning and muscle endurance set.
Stretches before exercise don't reduce the risk of injury, and I think lower the power of your muscles.
I'm not a fitness trainer....but I really disagree with that. Especially for people who are out of shape. Pre-workout stretching helps prevent serious muscle cramps, and helps increase your muscle extension. It may decrease the power of your muscles a little, but I think it helps your muscle stamina than just going straight into a workout.
Put it this way. Would you let a hotrod sit for 20 years, then turn it on a do a brake stand? No, because it's a machine, parts get brittle, gunk fills tubes and it puts stress on the motor to go to 100% immediately. So you turn the car on, let the engine warm, let the goop liquefy, let the parts get a little more pliable, pump the gas and rev the engine a few times....then you do a brake stand.
Seriously though, unless you're already in the habit of working out, being in shape and being "stretched", you should do the pre-exercise stretches. The post-workout stretches are really helpful too. I think if you're really committed, you'll do both and be better for it. He doesn't sound like he's trying to set weight records or anything.
I don't have any good links, because I learned all my stretches in high school and it would take a while to write them all down here. But keep looking, especially on Youtube, I'm sure there are workout stretch demonstrations there.