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Pretty sure it will go, However the PTO side of the crank is smaller on the 01 so you will need the 01 clutch also.
 
will a 2001 mc 800 carb motor mount in a 2003 900 carb chassie? if not what needs to be done.

yep will bolt right in but it does have the smaller taper crank which is not good. i have seen many of the even the bigger tapers break with any hp put to them. there was also a recall on the 01s pistons they had problems with the skirts falling off them
 
Dont see why it needs either motor mount? I am in the process of drop and rolling a 02 Chassis and the mounts stay the same? the jack shaft support bracket changes, maybe that moves the motor mount?
 
All I know is that the 2003 M-cat I had and the 2002 M-cat I currently have don't use the same motor mounts. I owned both sleds at the same time and looked at them in detail because I planned to do a factory style drop and roll to the 2002. I have since sold the 2003, but I know for sure that the rear motor mounts aren't the same. Below are the parts diagrams for both the 2001 and 2003 mountain cats and they are obviously different just looking at them.

Does it really matter though. The OP has the 2003, so it is just a matter of unbolting the 2003 mounts from the 2003 engine and putting them on the 2001 engine.

2001.gif 2003.gif
 
The diagrams in the last post are comparing EFI vs Carb engines which are different. The mount brackets on all the carb engines 800 and 900 will interchange.
 
Shows you should read the posts better. I had it in my head for some reason that the OP was putting a 2001 carb motor in a 2003 EFI sled. I see that was incorrect. My apologies.
 
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