wait, let me re-read what's your problem and why you would need r53 (which is bad).
emuNAND often doesn't work with r53, you need r52 !
edit: ok I understood what you meant. you think too ahead of the problem here.
r53 was suggested only because another user who is currently using r53 doesn't have the vWii unsync issue, and you wanted to test r53 too.
but other users who use r52 don't have sync issue either.
r52 and r53 shouldn't affect the controller differently. you have another issue, but you can try r53 before thinking about needing to set back emuNAND to r52 like if you already found the fix to your problem.
if you have unsync in emuNAND, that's another problem or issue (and might be normal if you created a new NAND).
if you use emuNAND in vWii (to load channels installed to emuNAND, or neek) you need to dump your system file to that emuNAND copy. the SYSCONF file contains the controller sync information.
if you lose sync when resyncing in emuNAND, that's probably caused by this file's conflict.
if you only want to test r53, don't install it in a new empty slot !
don't install it like you will need to keep multiple version at the same time for whatever reason and imagining a way to get used to switch slots every time you play something different.
just replace for example the slot249 with r53 ! do your tests, if it doesn't fix or improve (it should even be worse), then revert back and reinstall r52 in slot 249.
if it helps, then, keep r53 and you don't need r52 anymore.
r53 is not always bad. some HDD don't work with r53+emuNAND, some work. you'll need to test to know if r53 is good or bad for you, but it has no relation to the WiiUPro.
Edit :
Surprise! I didn't expect it before 2018.
1269_mod2 with WiiU gamepad support
http://www.mediafire.com/?74jbrzozleqnk
It has some issue :
1. Stick's diagonals are not working.
I don't know why ok I do, calibration range is different than gamecube sticks. but at least, it works, you can move the cursor and press the buttons. I'll try to fix it later.
2. cursor speed is very slow, you can change the speed from 0.18 to 0.5 in the GUI Settings. I'll made an automatic WiiVC detection to do speed x5 without needing to change the setting manually.
3. still no channel mode. didn't had time to debug it. (it finds how many channel is on NAND, but can't read the title from it. Maybe ES_ is working, but ISFS is not in IOS255? network is also not in IOS255?)
improvement: it should boot even faster.