first demux all the scenes you want get everything you'll be using into m2v and ac3 files.
the deleted scenes on disc 2 should be the same ratio as the movie, but you can check by either running two scenes together in Vdub or womble and seeing if they look the same, or using a screen capture like you've done and counting how many pixels wide the bars are (simple but effective methods)
to make the letterbox scenes anamorphic open them in vdubmod use the resize filter and resize to 720x428 use the Lanczos3 filter mode, check the box to expand the frame and enter the original size 720x 576 fill color black, the filter line should read:
720x576 720x576 resize(Lanczos3, lbox 720x576 #000000)
the hit the cropping button and set it to crop 125 lines from the top and bottom (Y1 offset, Y2 offset), the line will now read:
720x326 720x576 resize(Lanczos3, lbox 720x576 #000000)
run the filter and save as an AVI and re-encode as anamorphic pal in TMPEGEnc or similar, then you have anamorphic picture and no white text in the bars.
some numbers might need tweaking because the letterbox is not quite central to the screen, but it depends on the main feature, if you post a screenshot from each source where the bars can be clearly made out I will check the maths for you.
Also you said you have the feature as 5 m2v files, this is bad, as when you put the together in womble you will lose frames at the end of each section, you'll have to re demux the video. if you used DVD decrypter go into tool, settings, hit the IFO mode tab and set file splitting to 'none', now when you demux it will result in one file with the whole movie.
all of this info applies to pal and should not effect the play-back speed. I have no idea how to set the frame rate on womble it just set itself on mine based on the first bit of video I loaded, which was PAL and therefore 25fps.
I was going to do this myself but I'd really rather help you and benefit from it with less effort, are the scenes on disc 2 up to much, could you briefly describe them?
Thanks.