Injury & slight derailment

I injured my shoulder.  Simply put, I shrug my shoulder up when I do most upper body exercises.  This reduces the space between my arm (humerus) and the tip of my collarbone (acromion).  During and after exercise, it's normal for this area to be inflamed; however, that swelling combined with my tendency to squish it all together is causing the tendons in my rotator cuff to be worn down.

Consequently, I've started physical therapy and stopped all lifting from the waist up.

When I stopped running back in 2002 (after only starting in 2001), I never missed it.  Not for a minute.  I never thought I'd miss lifting either, but I do.  I don't know how long it takes for one's muscles to significantly atrophy, but I'm convinced that I'm getting weaker with every passing day.

And this brings me to the snowballing problem.  I'm not lifting, so I'm not putting as much effort into my nutrition.  I should be increasing my diligence, but instead I'm skipping days of food logging, snacking on high calorie foods, and not watching my macronutrient distribution (i.e., getting roughly 40/40/20% from protein/carbs/fat, respectively).  I've all-but-abandoned my weight loss spreadsheet and will have to put in some dummy numbers.

The optimistic take on this is that I've been able to concentrate on my running.  I'm still training for the Broad Street Run and that's going well.  Slow, but well.  I'm still weighing myself daily, and have lost a couple pounds over the last 3 weeks that I've been slacking.  So it's back on the wagon for me again.  When I started, I really wanted to be in fair shape for when we opened the pool - basically, not be embarrassed to go in my own pool.  Just working out and sticking with a diet for this long (6 months, 40 pounds) has given me the self-confidence to be able to swim in front of others, but I'm still going to have a bit of a gut.  I have 10 weeks until pool season starts.  Best case scenario is that I'm 20 pounds lighter then, and that only puts me 7-12 pounds away from my goal of <=15% body fat - unless my shoulder injury has caused my lean mass to plummet.