I am interested in installing a high output alternator on my 2004 Rubicon.  I have found several different models ranging from $300 to $1100. I am looking for recommendations on model and installation tips. Will these devices damage the computer?  

What objectives are you trying to meet?

A second battery with an isolator might fulfill your needs??  

I am installing additional lights, electric fan, winch (already installed) and stereo. Already have dual battery setup. I can probably get away with OE but have my mind set on upgrade.  

Well there are good ones and bad ones. And price is probably the best indicator.

The cheaper ones are not really hi output, don't have larger cases to support larger windings and don't put out higher amps at idle.

Get one with an external regulator. Hi amp alternators generate more heat and heat kills regulators.

If you have dual batteries already how are you isolating them? A solinode configuration as opposed to a solid state isolator allows for greater power because of the inefficency of the solid state type.

Painless wiring has a nice switch and solinode setup for battery isolating. FYI.

An electric cooling fan is a bad idea. They don't provide adequate cooling at low speeds. They are for light duty cooling needs, not for trucks and crawling 4x4s. If you want one because you think you'll get more horsepower, well I'm probably just wasting space.

Moving air requires energy. The energy comes from the engine. The fan either loads the alternator or loads the engine directly.

When cooling is not required the thermostaic clutch allows nearly free turning of the fan.