When I did my v5 rig, I first got it working on the stock display and firmware. After verifying that all was working, then I did the modifications needed for the display change and the KD8CEC firmware updates. The firmware from CEC must match the display. So if you have the Nextion display, then I would do both the display and the Raduino (Nano) upgrade at the same time. If you do it changing first to the KD8CEC firmware on the Raduino Nano, and not change the display, you need to load a different version than the Nextion display version. Not really much value in doing the extra load of the firmware, as the things you are changing will need to be redone when you change the display.
If you do not have the display, and want to use the memory manager software, then upgrading to the KD8CEC firmware for the 16x2 parallel input software will at least get you going on using the Memory Manager and allowing you to operate some of the digital modes. Just be sure you get the correct version (read the .txt file info file in the CEC software zip file).
The case that you bought may have some of the wiring different than stock,so you need to verify with the supplier on how to wire the new display. For me, with an off the shelf generic case, it was simply wiring up a set of header pins to take the place of the 16x2 display soldering the correct wires from the Nextion display to it. Then download the software to the Nano and a microSD card for the Nextion.
The programming is best done with the Hexloader program for the Nano in the Raduino. Here again make sure you have the correct program file, as there is one for each type of display.
The next hurdle is to get the tft correct (there are two version for each size display. If you have a basic display you need the basic tft file, and if an enhanced display you need the enhanced tft file. Again make sure you read the file info from the CEC zip file. I would also recommend that you use no more than a 16gb microSD card. That way the file system will be correct. There are ways to make higher capacity cards work, however the 8 or 16 gb are so cheap, just get one of those.
The above are my experiences, others may have different ones and different recommendations Please check out for yourself as it is all at your own risk.