convert an auto to a manual
 

Can it be done easily?

Is there any difference between the engines from a manual or automatic?

the engine no. the wiring harness, DME, and a host other things yes - if you are looking at just the engine - there will be minor differences but nothing to stop an engine swap since you will have to purchase the wiring harness and DME separately (or use a stand along EMS)

the usual advice is to sell the car and buy a Manual if you are thinking about a auto -> manual swap in a 964 or 993

That's what i thought.