If you wana replace functions with your own, I could patch them in for you, as long as they are shorter than the original one. (if it is longer, or contains string or large data, then you will need my tool)
Also, doesn't IDA Pro show you the function inputs?
Oh and here is a quick POC of my tool:
I modified the sample project helloJni (which basically displays a string from JNI to screen), it now calls a function that return a string. This function is called Vic (short for victim). by modifing the apk after it is build I can replace with my own function, called inj (inject).
Any way, here is how I had to modify it:
1- change AndroidManifest.xml to set android:debuggable to true (this is a must)
2- modified HelloJni.smali so it would call my library: libsotool.so
3- add my library to the apk, sign and install
now whenever vic() is called, the call is redirected to inj()
if you like I can email the source of sotool but you need to give me a few hours (need some sleep 3am here).