Couple Exercise Questions

The only one I can comment on is the HRM, I usually stop it after my cool down.

On the breathing - start slow. Really, run as slow as you need to in order to keep breathing. Your speed will increase gradually over time.

Pay attention to how you're breathing - if you're breathing and your shoulders are moving, then you are breathing wrong. You should be breathing with your diaphragm, and feeling your stomach going out. That way you utilize your lungs all the way.

If you are having trouble breathing while you are running, without know all of the specific details about you running, my first thought is, run slower. Unless you are doing tempo or interval runs, you should be able to comfortably talk while you are running without having to gasp for air.

Second questions...As a beginning runner, is there a technique to help me breath better? It seems I can't get past a certain point and I am winded and feel like I have to stop. I'm not sure if it's in my head that I can't go any further or not, but I don't feel like I'm improving at all.

When you start out, it’s HARD! Even if you think you’re fit, running is so different to anything else you’ve done before you will get out of breath quickly. Stick with it. Can’t manage a minute? Go slow. Still can’t? GO SLOWER!

That's from my beginner's running tips here:
http://www.myfitnesspal.com/blog/BerryH/view/20-things-i-wish-i-d-known-about-running-when-i-started-103936

Also find a rhythm that suits you. I breathe in over three steps and out over the next three - if I need to breath more often I know I'm going too fast. Some people prefer two in, two out.

If you're 'training' to the point that you find that you don't need any rest, and consistently carry out the same workout the next day without a drop off in performance, then I would say you are fine. I'd also point out that you could be spending your training time more effectively by selecting more challenging exercises if strength or muscular endurance is your aim. It's a nice workout for active rest during cardio intervals though, but may impact any strength training you follow.

Like others have said with the breathing, it is most likely that you are running too fast for your current level of fitness. You need to either reduce the intensity or the duration of your efforts.
If you're panicking or hyperventilating, then the streams of 'breathing technique' advice that will appear on this thread may be relevant, but it's likely that you're just not fit enough yet.

I use heart rate as an indicator of whether I'm actually cooled down or not. One of the fundamental purposes of a cool down is to aid the heart returning to it's normal level, so keeping it on will allow you to monitor this. Feel free to stop at a level under 120BPM for most people.

If you are having trouble breathing while you are running, without know all of the specific details about you running, my first thought is, run slower. Unless you are doing tempo or interval runs, you should be able to comfortably talk while you are running without having to gasp for air.

THIS

run slower - even if you're doing intervals, take your time to warm up at a "conversational pace" - meaning, you should be able to have a conversation with someone... shoot for long slow efforts first, and you'll get more comfortable as your cardiovascular improves... then you can mix in speed and interval work. always warm up and cool down - your body truly needs it... it will help you perform and recovery better.

it's fine to do calisthenics everyday, yes, but it's best to work another area for "active recovery" if you're particularly sore in one area. as far as your weight, reps and sets, they sound fine, but this is very individual so I would go by your body's response - are you particularly sore or something? are you getting sick? not recovering well? you should definitely eat a 200-300 calorie recovery meal after - you need something with a 4:1 carb to protein ratio and you need to get it in you within 30mins of the activity. this was the biggest thing I noticed to affect my recovery - that and adequate sleep. you don't get fitter/stronger with the actual workout, you do so during the recovery, so recover well, but don't just do nothing... think active less intense recovery - a swim, a very light jog or brisk walk, something to get the blood moving.

wear your HR monitor during the whole activity, including cool down... you want to watch to see how long it takes you to recover... do you know what your recovery range is? do you know what you max is? as you get fitter, you're HR will bounce back and recover quicker, so this is a good thing to keep your eye on.

First question...Is it OK to do calisthenics every day? I know you are supposed to give your muscles a break after weight lifting, but what about squats and lunges and abs. I don't do 100's a day or anything, but if I do like, 2 sets of 15, with weights, is that OK? I have kind of worked it in as Interval Training with my treadmill.

If you aren't going to failure, sure. At that low of a volume its no big deal.

But many people are irrationally scared of overtraining. Even going heavy you can lift every day. Concepts like Smolov, Bulgarian training, and Grease the Groove challenge the typical overtraining rules, and all of them are noted to work quite well.

Certainly true, but the one thing about it is that people training like that are probably eating a surplus rather than a deficit which would improve their recovery over someone who is intentionally undereating.

1) I've been told not to do the same part of the body on consecutive days but I'm not sure what the current info is on that. Seems like most folks on here agree that it's ok as long as you're not working to failure and I think that's probably true. It might help to know how much weight you use...

2) I agree wtih the advice above about pacing your breathing with your footfalls. I do a breath in then out for every two - so like that one person said, if you're starting with your left foot, breath in when it hits then breath out when the left foot hits again. Some do three, it depends on what works for you. This should help with the speed advice - you shouldn't be able to go too fast when you pace like this. Something that helps me is to count my footfalls so I get a good rhythm in my head and after a bit it becomes second nature. For some reason, the first 10 minutes (or mile) is the worst because you need to push past the breathing weirdness and getting your form and everything just right but after that, it seems to come very naturally.

You can try breathing in through your nose and out through you mouth but I know from personal experience that doesn't work for everyone. If you're like me and can't get enough air through your nose (seriously, I have collapsed/droopy nostrils, it's not possible) make sure you're breathing evenly and deeply enough to avoid any side stitches. If they happen, walk for a minute or two to catch your breath then start running again.

3) I leave mine running until I'm done stretching/cooling down.

It does get easier after a while but even then, we all have our bad run days...they just happen.