Does anyone knows of any good software or tools to do this?
Every manufacturer's stuff is different. You are going to have to get really specific.
I'm working for a company that bypasses DPF/DEF/SCR systems. Forget about messing up your ECU. You plug-in the device and computer 'thinks' that everything is working fine. I don't want to get blocked on my first post so let me know on priv if you need any help.