I am assuming the IDI is a 92-94 Yes? You mentioned the PSD is a 95, but no year on the IDI.
Assuming the IDI is the same body style, not a bricknose, the existing VSS in the chassis harness should be fine.
The transmission harness should be a sub-harness that plugs into the main underhood harness, so you can swap it in when you change the underhood harness. The harness swap (trans harness from the IDI) with the 5 speed will negate the E4OD's MLPS input for park/neutral start. In the vicinity of the steering column, you will find a connector with a bypass plug inserted into it. Remove the plug and connect the harness to the clutch safety switch.
You will need to keep the bellhousing spacer for the swap, but the crank spacer for the flexplate isn't needed.