I think this sound nice :) You say that you found this difficult, the first thing that I noticed in this piece was the harmonic rhythm. Have you thought about that?
When you write an in the baroque style, the harmonic rhythm is everything. Themes are bound by the harmonic rhythm. In this case your harmonic rhythm is not enough grounded, and that is why its hard to write. When writing a baroque theme, you need to think the entire structure at once, the rhythm, and the harmonies. If you do this, it will be easy to write good counterpoint :)