You basically have to "re-root" the phone again to get su in recovery. The sequence of getting into shell is also VERY important. So you would have to start the root process over again.
When ever you go back into root in recovery after you have root. You do not have to repush the Superuser.apk and the chmod the permissions. The all stick from the first time. At least for me.
And for those who want it....
Code:
#Remove FriendStream
/system/bin/rm /system/app/FriendStream.apk
/system/bin/rm /system/app/com.htc.FriendStreamWidget.apk
#Remove Peep
/system/bin/rm /system/app/com.htc.TwitterWidget.apk
/system/bin/rm /system/app/HtcTwitter.apk
#Remove FootPrints
/system/bin/rm /system/app/HtcFootprintsWidget.apk
/system/bin/rm /system/app/HtcFootprints.apk
#Remove Stocks
/system/bin/rm /system/app/Stock.apk
/system/bin/rm /system/app/com.htc.StockWidget.apk
#Remove Visual Voice Mail, The Icon Remains
/system/bin/rm /system/app/VVM.apk
#Remove Quick Office and PDF Viewer.
/system/bin/rm /system/app/Quickoffice.apk
/system/bin/rm /system/app/PDFViewer.apk
#Remove Vzw BackUp Assistant
##WARNING## You MUST Do A Factory Reset If You Remove These
## Or You Will Have Force Close Problem in Accounts & Sync
/system/bin/rm /system/app/VzWBAClient.apk
/system/bin/rm /system/app/VzWBAService.apk
#Remove FaceBook, Updated Version In Market
/system/bin/rm /system/app/Facebook.apk
/system/bin/rm /system/app/HtcFacebook.apk
#Remove YouTube
/system/bin/rm /system/app/YouTube.apk
#Remove Calculator
/system/bin/rm /system/app/Calculator.apk
#Remove Teeter
/system/bin/rm /system/app/teeter.apk