Please Scroll Down to See Forums Below 
It's almost redundant to say, but stretching before every workout is just way underrated. I used to do 7 min. on the bike and considered myself warmed up. I also used to think a life of slowly accelerating chronic pains was unavoidable.
Ok I'm more than a few years older than you guys but if my beat up physique can recover then yours should have an easy time of it or you need to visit the doc.
Obviously the whole idea is to increase mobility and reduce pain. YTWL, bodyweight lunges, hip crossover, lying opposites, etc, etc. 6-8 of your choice gives your body the chance to work through it's natural range of motion before you start taxing it.
Another thing I used to do when I wasn't 100% was to ignore the problem by working around it. Just substitute one exercise for anther and pretend it's business as usual when it obviously wasn't. Stop pushing and let yourself heal.
I spent too much time spinning my wheels before I learned to back off and work on increasing overall conditioning. Patience is required but otherwise your just setting yourself up for more grief by stressing out the rest of your system as well. I would always remember the theme from Rocky: "Getting stronger..." to keep me on track. []
The holistic approach rather than body part orientation works better for getting well just as it does for normal weight training.
Increase rep ranges and intensity by reducing time between sets. A more MMA type workout. The old fashioned grouping exercises by apposite muscle (A1- bench A2- row; B1- leg press B2- GHR, etc.) was helpful.
Intense or DC stretching is superb at this time and, of course, visit your friend the foam roller after every workout.
I don't want to preach to the OP. Korin, and SL also, you both impress me as having a superior sense of knowing what you want and knowing how to achieve it. On the other hand, in the face of the unexpected, I hope you'll consider some of my ideas.
It amazes me. I see the same guys everyday at the gym and none of them do any sort of mobility/flexibility or even a general warm up. I have a daily ritual.
Warm up
5 minutes on bike
25 broom dislocates
25 twists holding the broom extending in front of my body
15 second hang from chin bar
10-15 twists hanging from chin bar
15 forward leg swings x 2
15 side leg swings x 2
15 OHS with broom
Cool down
Static stretches...
Warrior hip flexor stretch 3-5 x 15-30 seconds each
Cossacks 3-5 x 15-30 seconds
ham stretches 3-5 x 15-30 seconds
Piriformis/glute stretch 3-5 x 15-30 seconds
more dislocates
My warm up takes around 15 minutes and I will skip the gym altogether before I skip my warm up. It's that important to me. Sometimes the static stretches are done at home depending on time, but they get done. On days i do cardio only (2-3x a week) I will go through this whole routine after. It great speeds up my recovery.
Oh and I foam roll at home before every workout and whenever I feel overly tight in my hips/scap. The foam roller is not very enjoyable and sometimes I have to really talk myself into doing it. Necessary evil.
