I was wondering what the amp rating on a stock 2k1 civic alternator and what would be some of the benfits of upgrading the alternator to higher amp

 
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Answer to your first question would be in your owners manual, i know that doesnt help but i dont want to spit out a number if im not sure. (i want to say something like 120 - 140 amp though, rough estimate)

Second question would be that your battery stays fully charged during normal driving conditions, and you will not notice wuite as much of a power loss when using multiple high draw components (turning on headlights, rolling down windows and opening your sunroof while honking your horn and blasting your 600 watt stereo system all at the same time, oh yea, all while using your windshield wipers and defrosting your rear window)

 
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- Not exactly sure here, but I think that upgrading to a high output alternator will take a way a little bit of horsepower (the opposite of an alternator pulley adding horses because the alternator isn't putting out as much power)
The only reason you would need to get a higher output alternator is if you are running a BIG sound system, or a lot of ICE.

 
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Dead right GhettoCivic. You would also cut into your Miles Per Gallon with a high amp alt. I would run all the electic goodies with the stock alt and check that the battery will hold the volts that it does without all the goodies on before you go and change out the alt.

Food for thought.

Would the factory wire harness (and all the fusible links built into it) carry the power of a high output alt if you did go with one?

 
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80 amp alternator stock, upgrading will not hurt your fuel or horsepower.

 
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80 amp cold, 70 amp hot... hot rating is more realistic since your car will be running