Just go into shipsizes.txt, and add a new ability!
If SE4 dosen't choke on the negative movement bonus, you could do it by adding an ability "ship - movement bonus" (check abilities.txt for correct spelling), set amount one to "-1", and amount two to "3" (so it dosen't conflict with engine/solarsail bonuses).
Load SE4, and see if it works
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Problems you will encounter:
- what happens to an engineless ship?
If you want to make different ships go slower, I would suggest using the "engines per move" setting. Give engines 10 standard movement, and make the hulls require 10 engines per move or more.