If the leftover files you are talking about are the ones in the /usr/src directory because you originally installed it **from a .src.rpm**, I have just gone and deleted those all from the SPECS/RPMS/BUILD etc... directories after uninstalling the package. To me, they seem like leftover installation files once the package is installed. You may first want to find out if this is OK to do (for any .src.rpm package for that matter). This is from one newbie to another, so take it with a grain of salt.
However, if you just installed wine from an ordinary .i386.rpm, (not a source rpm), then just remove your .wine directory (rm -rf ~/.wine) and type "wine" and it will be created anew. then you can edit the config file and do a "wineboot". You will loose all your programs installed on the fake win drive and any customizations you made in the config file.
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