Those 2 engines are the same, there may be some minor sensor changes,
the only one I am aware of is there is a crank position sensor on some models
but I think it started with the 96 so it may be no big deal, look at the front
of the engine just behind the crank pulley for a U shaped edge on the oil pan
and a wire going in there, that is where it lives.
As far as the Manual / Auto swap, you will need to swap computers to make
the trans shift correctly but on the plus side, you have both complete vehicles
so all the bits are there for the swapping, so unless you break something no
parts should be needed for the conversion
Good Luck
Wild