Sounds like you've got a forward shoulder kind of thing going on. Get the bike fit, or otherwise make sure your bike is adjusted right first and foremost. Too long a reach can make you slide your shoulder girdles forward and up. Play with the helmet visor if you think it's making you tilt your head up too far (that would strain the muscles in your neck and shoulders).
I'm thinking your mid scap pain sounds more postural than mechanical. Basically, it's like slouching on the bike (on those flat trails you describe) rather than being in good active posture (in the woods you describe).
Try riding on one of your flat bike trails while concentrating on keeping your back neutral and holding your shoulderblades pulled down and back. (like you're trying to drag your shoulderblades to the hooks of your bra) Or imagine you are Dolly Parton/Mae West and concentrate on keeping "the girls" up and your neck long and elegant. The muscle you're trying to kick in is the lower trapezius.
If changing the muscle force balance from upper trap/levator scapulae to lower trap helps, then work on that until it becomes a habit. If it helps but you can't maintain it, or it doesn't help at all, I'd recommend going to a sports PT who works with bikers and does bike fits.
And if you need to give those grumpy muscles some love, try the tennis ball trick. Put a tennis ball in a sock. Dangle it over your shoulder so the ball is over a tingly-burning-grumpy bit. Back into a wall so the tennis ball is between you and the wall. You can squirm around like a bear scratching his back on a tree, or just lean on the ball to put pressure on the spot. Much easier than trying to reach it with your arms!
"If Americans want to live the American Dream, they should go to Denmark." - Richard Wilkinson