I have a Launch X431V+ scan tool, now 5 years old. It goes in and checks every module in the car and gives feedback while also having the ability to program some of the modules. 2 way communication. It allowed me to program or at least reset my transmission on new install. The BCM, ABS and many other systems can all be checked. Several of the higher end scan tools can do this for you. I would get one and see exactly where your problems are.
The scan tool allows you to flow check every injector, watch misfires on each cylinder, watch fuel pressure, watch the knock sensor voltages, read O2 sensors real time to see exactly what your cats are doing and how well the engine is burning along with hundreds of other features. A tool like this is expensive though, $1300 up front and $400 a year for updates. There may be many other options out there that do the same or more for you.
When working on these engines there are so many connections that are critical for proper performance. Almost every job I have done I think I am 100% finished and then plug in the scan tool and it will show a sensor is not reading. Duh, it is not plugged in yet or a wire was pinched as the job was done. It is always nice when you get it right the first time but it does not always happen and the scan tool is a mandatory check when you do these jobs. Hope you figure it out quickly.