flexible 0 awg is easier to work with - that means the stuff you get at farm & fleet will work but be a bear to route. car audio power wire is super flexible.
be sure to get the proper ring terminals, the alt stud uses a 1/4" ring hole while 3/8" will usually work for everything else. i like to solder then heat shrink the connections unless i'm using an enclosed ring terminal with heat shrink - no exposed copper.
properly done, no negative effects. poor wire routing, poor wire protection, poor grounding locations can all have negative effects.
just use factory grounding locations on the frame and engine block, protect with high-temp split loom, route and secure like factory, and you're good. when you're done it should look like it came that way from the factory.