@Eborne1 as I understand it, to clarify (maybe): for the remainder of this combat, only the second shot is taken at -2.
The general rule, and in all cases going forward, is that Extra Shot gives you a second shot but imposes a -2 penalty to both, so -2/-2 as a standard attack action, and further modified by TWF to give you a third attack, which I guess means penalties of -4/-4/-4 if you have the feat?