Run MAMEWAH v0.954b first to get the config files written.
Then run MAMEWAH Set-up. When MW set up runs it makes a note of what version of MAMEWAH you have and stores this in the windows registry.
Exit MW Set-up and overwrite v0.954b of MAMEWAH with v0.962.
Then run MW set-up again.
As it loads it checks what version of MAMEWAH it used last to the version that you are using now and if they do not match it should update all the config files to match.
Once you have selected the folder that MAMEWAH is installed in you do not have to set this again.
If you upgrade MAMEWAH all you have to do is start MW Set-up and everything should get done for you.
Hope this helps

You may have to modify the registry settings for MW Set-up. Because it may have the wrong version number saved in there.
If you run regedit and goto 'HKEY_CURRENT_USER\Software\VB and VBA Program Settings\MAMEWAHSetup\Start' in the box on the right you will find a Key called 'Version' if you are going to run v0.954b of MAMEWAH first modify this setting to 0.9.0.54