Green Day tunes in drop D as well, so best to keep that in mind. If I remember correctly, mike tends to pick behind the pickup when he plays, or at least used to when dookie came out (gives a higher tone), but then again back then he used to use a gibson ripper or grabber (different tone entirely). As for software and eq settings... I don't know about that, so I won't try to give any comment on those things.
Actually the play in Eb.