The only issue I know of when un bolting the steering column is that if you drop it down too low, you will damage the input shaft. A precaution so that this does not happen is to simply sit in on the drivers seat. Any lower then this, you could do damage... like I did.
When you pull the dash forward, be cautious that the wire looms are not caught on anything, and don't let the dash hang from the wire looms, give it some support.
All ECU's have a sticker on them, with a particular code, giving date auto/manual etc.
From memory, the Auto code ends in "B" and the manual ends in "A"... however, don't quote me on that, might pay to give Ford a call.
As for identifying the box, I'm pretty sure it should have a date stamped on the side.
Good Luck, and may patience be with you.
PS: YOUR GONNA LOVE THE 5 SPEED!!!!!