One more thing. Should I update my firmware back to 4.2 or stick with 4.1?
The good news is… wait for it… when you reapply the firmware, you’re going to revert to 3.5" dimensions.
So now we know what the problem is. It’s not your hardware or your setup, it’s 4.2 related. I don’t know what changes you need to make to that app to be able to make it work on 4.2 but I can tell you the core function you need to get working is in SetLCDConfigurations().
4.1 is the only supported way to use WiFi at the moment. That’d be a good reason/excuse to stay on 4.1 if you have the WiFi module 
I’m still not sure on what to change in the LCD code. There seems to be just values in the function that you mentioned, and no indication of what to change to change frameworks. Any ides?
Anyone?
We tested all our products with 480x272 4.3" displays so I am not sure why you are having problems.