Simplest and cheapest way would be to hire/borrow a petrol disc cutter with a diamond blade and run 4 slots up the floor to give you 2 channels for the wheels. Cut between each channel around 15mm slots with the cutter so you end up with a dozen or so long slots on each channel, you can then break the raised 'teeth' easily with a crow bar or something.
Disadvantages are it's a dirty job, very dusty (some cutters have a water feature that help greatly) and rain may creep under the door so you'll have water filled trenches?
Looks council to me? They won't like you lifting the roof.
Changing the doors is less bodgy but will you still have the clearance?
Also check the internal roof joists are not slightly lower than the opening.