@killswitche,
Get yourself a coach, or coaches. Whether it be a:
- life coach
- leadership coach
- conflict coach
And I mean one that will help you go through the motions - who will not just explain how to do it to you, but help you practice, over and over again. You've gotten into bad habits that have been ingrained - retraining will take time and effort. Luckily, as both a PhD and Engineer, you should be able to afford it.
I'd go for the conflict coach first, as what you appear to want most, is learn how to be assertive.