The wire colors for the Monsoon amp connector are listed in the Monsoon FAQ sticky at the top of the section but you don't need them. Get yourself the proper harness adapter (available at any auto parts store or even WalMart) and connect it color for color to the new head unit (i.e. red to red, yellow to yellow, etc.). Then the whole thing just plugs into the factory connector. The aftermarket head unit will work just fine with the rest of the Monsoon system so there is no reason to bypass the amp.
Steering wheel controls using an infrared adapter are so last year. These days almost all head units come with a wired steering wheel control connection. Get the adapter that matches the brand of stereo (SWI-PS for Pioneer and Sony, SWI-JACK for JVC, Alpine, Clarion, and Kenwood, etc.) and it will connect directly to the head unit harness without the need for an IR remote.