OK, I think I know in general terms what you are thinking about. & to be honest I've thought about something similar myself.
As far as making the sealed containers accessible, the answer would probably be no, not without major mods to the containers themselves and probably the loading/restraint systems as they are basically made to fit very closely into the specific shape of the hold, and to pass through a specific size of cargo door.
Can you change the headroom by moving the floor up? I'd say that one falls into the "definite maybe" category. The current fuselage cross member locations will have been analysed to death by classical and computer based stress analysis and placed in their current locations as optimal for stress distribution for specific loading cases. If you change [reduce] what the load limits are going to be by taking on SLF only rather than freight, then the locations of the cross members could be changed, but you'd need to go through the analysis cycle again, as well as actually re-building the aircraft if the answers came out OK. This is where major expense would come in as I strongly suspect that the fuselage would need to be completely held in a jig to remove the existing cross members and repladce them with alternative ones at different locations.
As for the dimensions, you might find this link useful....
FlyingCorral.com - 747 Aircraft Information
Like I say, I think I know what you are thinking about & it's probably viable for some aspects, but I think that the commercial aspects of the changes would outweigh the maybe limited benefits. A better bang for your buck might be to think about a standard ISO container in transit by sea.