Got round to having my shoulder looked at. Had a sonar, and turns out my impingement is caused by a calcified tendon - I got injured somehow a while back (can't for the life of me remember it), and good guy body decided to "fix" itself. I've been referred to a specialist whom I'll only see mid December to figure out what to do to sort it out permanently.
Against my better judgement, I decided that I'd been idle for long enough because of it, so joined a local gym about a month ago. Been out of it for a while, so decided to get my body used to moving again by cycling and rowing. Slowly increased the duration over a 2 week period, and then decided to start 5x5 again - if it hurt, I'd stop. I've finished the 2nd week now, and haven't had any pain while lifting - sure, I've started the program right at the beginning, so not going heavy yet. But, my shoulder actually feels better? As in the pain when idle and moving about normally has drastically reduced!
Go figure.