I don't think there's an option to choose what one can & cannot transfer with WET. If you want to really start afresh, do a fresh install & manual transfer of the relevant data. This can be laborious though, but one which I always find rewarding by the end of it.
If you had those website problems in IE, have you tried an alternative web browser? Like Firefox click here or Opera click here for instance? Give them a go & let us know if there's any change. G