Yes, you can change things like that.
Back in the Midway mission example, if you are going to change the unit from a submarine to a ship the mission needs to know which ship you're going to use.
The name=, class=, the type=, the origin= "American, Japanese or a Martian if you're playing as one of them." the side=, 0 is for America and 2 is for Japan, I don't know what side the Martians are on though.
Don't forget about the Height, Height=-18.000000 is periscope depth, Height=0.000000 is on top of the sea. Play about with it and you'll eventually get it working.
[Unit 1]
Name=USS Grouper
Class=SSSalmon
Type=200
Origin=American
Side=0
Commander=1
CargoExt=-1
CargoInt=-1
CfgDate=19420301
DeleteOnLastWaypoint=false
DockedShip=false
GameEntryDate=19380315
GameEntryTime=0
GameExitDate=19451231
GameExitTime=0
EvolveFromEntryDate=false
Long=-21493264.000000
Lat=3726281.000000
Height=-18.000000
Heading=4.081214
Speed=5.000000
CrewRating=3
DelayMin=0
ReportPosMin=-1
ReportPosProbability=100
RandStartRadius=0.000000
NextWP=0