Good stuff thus far. But just in case the OP isn’t confused/bewildered enough yet, I’ll add my thoughts as well.
Working with the goals as stated in your OP:
“1) when I was 17 I could run 45 minutes straight…I’d like to get back to that and push it to an hour”
I’m not nearly as phobic about running as some commenters. I run for 60 minutes once every four or five days (if I may be allowed to stretch the definition of the word ‘running’ to include ‘brisk stiff-legged limping’). But I do agree with the contention that too much running will not advance the ball vis a vis reaching your physique-related goals, and in fact may interfere with doing so. So if you like to run, you want to run, by all means run. But make running a secondary activity. Think of yourself as a weightlifter who runs, not a runner who lifts weights.
“2) I’ve had a muffin top since I was 8…I’d like to get rid of that”
There’s not much wiggle room re achieving this goal: You must average a fairly significant caloric deficit for a fairly significant period of time. There are any number of ways to do this; my personal favorite is carb cycling, about which you can find a great deal of info on this site.
“3) I really like the way toned arms and nice shoulders look…and so does my girlfriend”
I assume you also like the way toned [insert other bodypart names here] look as well, so in that regard I agree with previous posters that your routine should address more than just these specific bodyparts. However, I would respectfully disagree that a power/strength program, with its emphasis on the squat and deadlift, is the best approach for a young woman with undermuscled (per her) upper limbs and overmuscled (ditto) thighs to ‘tone up.’ Not saying you shouldn’t squat and/or deadlift; rather, that the singleminded pursuit of adding weight to these lifts (which constitutes both the only goal and the only outcome metric of such programs) is not the best way to get bigger arms/delts & smaller thighs.
“4) I have power-house legs (huge thighs)…can I shrink the size without losing the muscle?”
I am always leery when someone says ‘I have too much muscle in my [bodypart],’ or ‘I gain muscle too easily in my [bodypart].’ Ask anyone who has made a concerted effort to get them–hyooge muscles are dauntingly, maddeningly difficult to achieve. This is because the human body seeks homeostasis and efficiency, and ‘extra’ muscle is metabolically very expensive to create and maintain. This is especially true for females, as their hormonal profiles tend to be less favorable than are males for building/maintaining muscles.
In my experience, when a woman makes such a claim, what’s usually going on is she has ‘stubborn fat’ (to use Lyle McDonald’s term) on her thighs. For hormonal and anatomic reasons, stubborn-fat stores are less amenable to being accessed during a cut. Thus, when a woman afflicted with stubborn fat loses weight, she tends to lose it from everywhere but these stubborn stores–the result being that it looks as if her thighs have gotten larger (ie, because everywhere else has gotten smaller). Conversely, if she inadvertently increases her caloric intake upon embarking on a vigorous exercise regimen (a common, albeit unintended and unwelcome, result of exercising more), these stubborn fat stores are the first to incorporate any excess calories, thus yielding the (false) impression of an exercise-induced increase in thigh muscle mass.
^If this is you, the first strategy in dealing with it is meticulous diet control; ie, making sure your caloric intake doesn’t creep up as a result of the extra hunger that will inevitably accompany your increase in physical activity. The second strategy consists of certain exercise, diet and supplement adjustments that can facilitate accessing these stubborn fat stores. However, you don’t need to worry about those until you’ve lost a lot of bodyfat everywhere but your thighs; eg, if your BF drops enough to show a 6-pack, but your thighs haven’t shrunk proportionally. We can help you cross that bridge should you get to it.
All that said, there does seem to be a subset of women who do tend to disproportionately gain muscle in their thighs. So if this is you, it is all the more reason to avoid embarking on an exercise program that emphasizes heavy squats.
“5) And yes…I’d like to look good naked…doesn’t everyone?”
As I am old enough to be your father, I will refrain from engaging with you on this topic. ;^)
Hope this helps. Best of luck reaching your goals.