; role = AI role (Generally affects the way in
; which computer players use the unit, but
; roles >= 5 will actually affect abilities
; of the unit)
; 0 = Attack
; 1 = Defend
; 2 = Naval Superiority
; 3 = Air Superiority
; 4 = Sea Transport
; 5 = Settle
; 6 = Diplomacy
; 7 = Trade
Nuclear Msl., nil, 1, 16.,1, 99a,0d, 1h,1f, 16,0, 0, Roc, 001000000000000
Diplomat, Esp, 0, 2.,0, 0a,0d, 1h,1f, 3,0, 6, Wri, 000000000000010
Spy, nil, 0, 3.,0, 0a,0d, 1h,1f, 3,0, 6, Esp, 000000000000011
Caravan, Cor, 0, 1.,0, 0a,1d, 1h,1f, 5,0, 7, Tra, 000000000000010
Freight, nil, 0, 2.,0, 0a,1d, 1h,1f, 5,0, 7, Cor, 000000000000010
This is an excerpt of the "rules.txt" -notice the number right before the prerequisite tech? -That's the unit "role". If your caravans and diplomats don't work, you should change these numbers to 7 and 6 respectively, regardless of the unit slot you're using.
The only units that are 100% dependant on the same slot is the spy and the freight, which won't give any extra bonus'es if placed somewhere else.
Missile type units should have the flag for "destroyed after attack" checked in the last binary row. It's all in the rules.txt, you should be able to figure it out from the brief explanation there. Nuke missiles should always have an attack of 99, regardless of the slot you use.
Hope this helps!
PS : You can download an upgrade to MGE from a link in the downloads section, if you like. This doesn't solve the above issue, but it does give you access to a whole line of additional unit types, and about 11 extra tech slots.