(perhaps it’s obvious – but...)
(a) First off, remember: Hesitation is the enemy. Whenever/wherever you run shirtless, take the shirt off decisively and keep it off, as if it’s the most natural thing in the world; you’ve been doing it all your life. The illusion of confidence can be beneficial.
(b) To shield from insecurity, try the ‘what are you looking at?’ technique. I don’t advocate hostility to those you encounter, of course. Rather, try a blank stare if you sense unwelcome attention. Let them question their own behaviour – not yours.
(c) Mental application is important: To fend off self-consciousness, concentrate intensely on what you’re doing and your surroundings – or on anything other than just that you’ve got your shirt off.
(d) Remember your posture! Keep your back and head up straight and your shoulders back – so nothing sags and you don’t slouch. This is one area where thinking about what you look like is going to help (well, I think so).
I hope this isn’t too patronizing – it helped me in my early twenties, I hope it could help others.