In theory, yes. You can edit the MIS files with a text editor and change the player's boat Height=-18 (or whatever) to =0 (zero). You can also change the ship's call, etc. Only problem with using a text editor, is that there isn't any error checking like the SH4MissionEditor (ME) in your game folder, which can be used also. "Run" the ME however you can, and point it to the Data / SingleMissions / SMxx Your Mission folder, and open the MIS file of the same name. You generally have to zoom in so that you can see what you're doing. Consult
Webster's Mission Building Tips... thread for links to ME info. You might find it easier to make your own missions for a better 'balance' against opponents. Even if you don't use the ME, read some of that ME info. If you're going to edit an existing mission file, be sure and make a back up of it first, just in case...