Partial answer on preserving Library structure, or at least recording it.

In Aperture for each folder or project give all photos in that container the name of the container.

E.g. if you have

folder - holidays
    folder - 1984
        Project Wreck Beach, BC
        Project Whistler, BC

Then you give the first project the keyword F_Holidays-P_1984-Wreck_Beach

Albums can work the same way. Give each album an A_ keyword. If you have folders of Albums,then they get keywords like F_Best-shots-A_West-Coast

My first thought was to do it in chunks: E.g. give everything in a folder F_Best-Shots, then label the abbum separately, but you would lose the hierarchy if you do this. Some you could deduce, but if you hundreds of containers....

After you have done this, write all keywords back to media, then, since you are going to lose your edits, select all images that have adjustments (Rule adjustments is applied)

If you think you may want to re-edit these export as a format that matches the bit-depth of the original. Avoid Jpeg for anything that you will re-edit. PNG, Tiff, PSD. If you have adjusted versions of JPEGS, I don't know how much you will lose on export.

Get your master file names in sync with your primary versions names. This will allow you later to get masters and derived pictures back together. You can do this with metadata batch change.