I am a baal teshuva through Chabad and began wearing tefillin with the Chabad kasher and davening Nusach Ari.
A few years ago, I left the chabad movement and became more affiliated with mainstream litvish yeshivishe circles and purchased new tefillin with the kesher in the way of the Ashkenaz minhag (and wrapping inwards) as well as began for daven nusach Ashkenaz.
Was this problamatic that I did this? And if yes, must I switch back to the Chabad ways?
My apologies that it took some time to get back to you, but i was away for some time.
Regarding your question, what you did was permitted, especially if you come from Ashkenazi descent, and you are essentially returning to the minhag of your ancestors. This is essentially what a baal teshuva should do, however if he wants he can adopt the minhagim of those who were mekarev him, but it is prefferable to keep to minhag of you ancestry.
Igros Moshe O:CH 2-24, Halichos Shlomo (Tefillah) 5 ftnt. 37.