yes, overwrite the IOS by running the installer again. you don't need to delete the old IOS first.
just install r52 instead of r53, and be sure to plug your USB to port0. (as only r53 support port1, but has few compatibility issues).
Also, note that some games just doesn't work on SD. (but should work on SD with USB adapter plugged into USB port 0)
I really REALLY hope you didn't REPLACE your IOS56-58
THAT'S NOT WHAT THE GUIDE IS TELLING YOU TO DO.
if you did that, you semi-bricked your vWii.
What the guide is telling you, is to "use the existing IOS 56-58" as base for the custom IOS. these base file are copied, patched and installed into slot 249-251.
as a result, you need to have :
IOS 56-58 official untouched
IOS 249-251 : copy of 56-58 patched
if you made a backup of your IOS before touching them, and you did a "proper" backup (no patch!), then you can restore them by using a
Wad manager and re-install the backup wad.
But before doing anything to IOS below 200, you should give us a syscheck report. we will see if they really are messed up or not.
Do NOT touch slot below 200 if not necessary.