Irrespective of your micro managing boss, I believe there are things you can do to alter your perceptions and responses to all the changes your company has gone through. That's commerce, im afraid. Things change and businesses get taken over or they merge and new people come in from outside.
Can you proactively look at how you work and think honestly "can I improve how I work? Can I try to collaborate and network a bit more?" It sounds like the big gap is your performance/development process where you and your manager should have periodic reviews and agree your objectives. You could use it as an opportunity to communicate with your manager about what you are working on, how you do things etc.
my boss really is picking on my performance and doesn't understand the way I do things and its mainly due to personality clash.
This is your perception, however can I suggest looking at it from your manager's point of view?
An example from me, I am in a new role and yesterday I was wrestling with a load of disparate incomplete information thrown at me which I was expected to make sense of, and add/update onto a tracker. When I took the matter to my manager, she was appalled that people were giving me such poor quality data in the first place. We agreed an action plan and she went away happy that I was being proactive to make her aware of my challenge. Sometimes transparency is an effective way of showing a manager A snapshot of your day, what's going well, what isn't and what you are doing to tackle challenges.
If your manager doesn't know how you do your job, then why not change that, they aren't an omni present mind reader 
I'm concerned you aren't covering this during your performance development reviews, presumably you have those, right?