Well now that I finally have enough hard drive space, and my the latest version of the editing software I am using will directly load .vob (DVD video files), I have been able to actually start editing the movie and cutting in my new visual effects.
I am using the DUNE: Third Stage Edition fanedit by PhineasBG and Nighthawks as a base since it contains all the deleted scenes though this edit also needs a good deal of tightening up in places.
The first thing I did was to replace the old 80's Universal logo with the current one since that was an easy fix and then add in my "Secret Report Within the Guild" shot.
I then moved the extended shot where Duke Leto talks to Duncan to a more sensible place (That allows for Duncan to be in the palace during the attack).
I am still trying to determine the best place for the discussion between Duke Leto and Thufir about what the locals called Paul - I was going to put it after the assassination attempt on Paul, but it may have to go elsewhere.
I recut the part where Alia attacks the Baron - the placing of the shot where she holds up the gom jabbar has always bothered me, so I moved to to directly after the Baron's reaction to being sliced, cutting his reaction into two. Also edited out the close up shot of Kyle MacLachlan "falling" down the cliff - that was always just a BAD effect.
Last night I went through and cut out all the effects shots and put them on a separate video track for easy identification - gonna be a lot of work - though obviously I am not going to replace every effect!!! LOL