I watch several episodes of Will & Grace everyday which are somewhat out of sequence. Last night I saw the pilot episode and saw two big differences: Will had long hair and Karen's voice was almost regular (lower). Was this only in the pilot, or did it go into season 1 as well?

Will's hair was only like that during the pilot episode. Karen's voice wasn't changed right away. After a few episodes it changed to what we know it as. I guess that is part of developing the characters.