I think it is not possible to access Camera2 API while using CameraEx, which is based on the first Camera API.
By manual focus, do you mean to be able to change the focus point (for instance touching on screen), or directly modifying focal length through the API? The first can still be done with Camera(1) API, according to what I have read.
For the second, and before doing anything, you should read this from
HERE
A given camera device may provide support at one of two levels: limited or full. If a device only supports the limited level, then Camera2 exposes a feature set that is roughly equivalent to the older Camera API, although with a cleaner and more efficient interface. Devices that implement the full level of support provide substantially improved capabilities over the older camera API. Applications that target the limited level devices will run unchanged on the full-level devices; if your application requires a full-level device for proper operation, declare the "android.hardware.camera.level.full" feature in your manifest.
In short, even using camera2 api, not all devices will give full-access to all of its capabilities. So if you are using a specific device for counting particles, you should first check if its hardware allows full-access
In case it does and you need manual focus (not the touch-assisted), perhaps it would be worth to make the setup from inline java porting only the required methods, assuming that there are not many. But it is not straightforward.