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A 2001 engine would not be a direct replacement like any engine up through the 993 model (~1997?). It is water cooled, so you'd need to put radiators somewhere. The transmission is very unlikely to fit at all w/out major body/frame work. I doubt that the motor mounts or transmission mounts are in the same locations. I would say that this would be as difficult as installing a Subaru or a Chevy engine. In short if you have to ask how hard, it is probably too hard. As a DIY project it would require body skills, fabrications skills, design skills, electrical skills, mechanical skills, and various other mad skillz.
The 996/997 engines have wet sump oil systems, which can have oil starvation problems under heavy cornering. The ultimate non-turbo drop-in motor swap would be the Varioram 3.6 motor from the 993.
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Mike
Searching for a new ride
'04 VW GTI 1.8T RIP 
'76 911S 3.0 RIP 
http://www.pelicanparts.com/gallery/BanjoMike
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