To be honest, it sounds like you were pretty rough on the replacement since you had to force it in and it’s not sitting flush. The button and cable are very sensitive and can micro fracture causing irreparable damage. First, I would try another screen. Sometimes the home button connection on the screen and or the connector to the mainboard can malfunction.
It’s definitely the touch IC and you don’t want to reball anything. You want to replace it completely. If you have micro soldering experience then this should not be a hard repair. However, this is not a DIY repair and you’ll want to find a reputable repair service in case you dont know how to micro solder.
You put your phone in the water on purpose? Is it not working at all? Apple will not replace your phone based on their claims of water resistance. So, that’s not an option. If anything, I would open the phone and clean it good with alcohol. If you have access to a shop that has an ultrasonic cleaner, I would get them to remove the board and clean it. Hopefully there is just light corrosion causing whatever issues you are having with the phone that will be remedied by an ultrasonic cleaning.
II know you can upgrade the flash drive storage by micro soldering a new chip, but that’s a difficult process. Apple’s memory management and iOS would probably not take advantage of the extra ram as it’s very efficient as is. What are you trying to accomplish? The iPad Pro is already a very quick device and iPads and iPhones have never been fast because of the amount of ram. It’s all about the processor.
Is there a foam pad on the battery connector? A lot of replacement batteries make this pad too thick and it causes your metal bracket over the battery connector to not sit flush. Remove that foam piece. The 3d touch barely working is the screen itself. Unless you purchased an original refurbished replacement screen your results will vary on 3d touch functionality. I’ve seen where the best aftermarket screens will still give me mixed results from working perfectly to being too sensitive or flat out not working.
Were all the small parts in it too such as charge port and power button cable etc? These parts either are bad from the beginning or can go bad easily. Are there any spots on the old housing where there is any type of grounding pad or covering that should have been transferred and wasnt?