So I've been working on losing weight (5'11 235, down from 265 in late June). Just did calorie restriction in July-Aug for the most part with some running and hiking mixed in 1-3 times a week, added a gym routine about a month ago (3x a week, usually 20-30min cardio and then lifting).

I've kind of been stuck at around 235 since I started going to the gym at the beginning of the month. I can feel muscle being added (ie, if I flex, i'm not as doughy) and my clothes fit better. I just signed up for MFP, and it seems like I've been eating less than the recommended amount (MFP says 1590,  if I eat my normal dinner tonight I'll probably be at 1200. I'd say on average I'm at between 1100 and 1500 most days).

I still have about 35lbs to lose. Is the stagnant scale I'm seeing a result of fat being replaced by muscle, or am I causing my body to go into some "starvation mode" by not eating enough? If that's the case, that doesn't really make sense to me. I would think the body would just burn more fat in that situation, but that doesn't seem to be the case based on what I've read. I sleep 7+ hrs a night, and have enough energy during the day at work, and for my workouts. From a science standpoint, why doesn't the body burn excess fat when it doesn't have enough calories, as opposed to stuff like muscle loss/organ deficiencies?

What you are noticing is better body composition.

You are building muscle which weighs a lot more than fat, which explains the clothes fitting better.

If i were you i would set a reasonable caloric goal, take some naked pics, and keep doing what your doing. Stop looking at the scale, its meaningless.

2 months from now you will have made progress because your body fat will be lower, not because the scale reads a lower number.

Not eating enough will screw with your hormones.

Try a couple of the TDEE calculators on line, get an idea of what you need to eat to maintain weight and eat 200-300 calories less per day while doing weight training an walking.

If you do not eat enough your body will hold onto more calories because it knows that it isn't getting enough fuel. If you are calorie deficient long enough your body will start to burn muscle and keep fat.

Remember that your body does not need much muscle mass to survive, but it does need fat to survive.

I'm no doctor,  but this sounds like the most accurate description of what's happening.  Cue the Biolayne/Layne Norton YouTube videos.

with adaquate fat and supplemental vitamin intake... its essentially a non-issue...

If your estimate is anywhere near correct, your caloric deficit is much too great. You're probably getting somewhere in the ballpark of a little over half the calories you need. Remember that the 2,000 daily figure is basically only accurate for a large woman or small man. A small caloric deficit will help you lose weight, but more is not better. Your progress is stalling because exercise and diet almost always involves diminishing returns. When you're really fat, almost anything works. If you're just fat(not really fat), you need to be more dialed in. When you want to go from fit to shredded, you have to be even more on the ball.

Fat loss is a marathon, not a sprint.

Try doing you cardio after you lift weights. Atleast thats what Ive always been told.

I'm 5' 7", 43 y/o, I went from 230 to 175 in a little over 4 months.  I went on a disciplined 1200 cals/day diet, high quality calories, limiting carb intake to less then 40 grams/day, 90 minutes of cardio everyday and as many sets of push ups and sits ups as I could work in. a performance multi-vitamin daily, no sugar, not even honey.  I lost about 3 pounds a wk.  I've kept it off for the past 2.5 years by running, biking, and eating smart.  I don't worry so much about carbs but I do poof up in the belly like its all full of jelly when I keep beer around the house and eat a lot of bread, rice, potatoes, etc.  

I would stall every now and then when I was loosing the weight, just make a small change in your routine and the weight loss resumes.

ETA:  I went to 90 minutes of cardio because for me that was teh magic number.  if I did 90 minutes the fat melted off like butter, anybody with eyes could see it.