I hope you are using GTK 1.4 If not go get it and download it. Open the map and go to the file menu where it says plugins and go down to bobtools. In bobtools you will see an option for bursh cleanup. Click brush cleanup and it will get rid of duplicate planes and should fix your other problem. After it tells you that is deleted x# of invalid/duplicate brushes, there will be a few brushes still selected...don't delete them, just hit escape a couple times and deslect them then save your map.
If you still have the node problem after that you may need to narrow down which brush is causing the problem. Delete a section/or suspected piece of your map and compile again. See if there are still errors. If there are then delete another section...and another...until you find the area that has the brush(s) that are causing the problem. That may be time consuming but it may be quicker than starting over.