ive had a couple of lupins die should I deadhead them or leave them as they are.
If its just the flower spike that has finished, then cut it down just below the bottom flower. If the whole plant is dead, its dead and you can pull it out.
Will a new flower grow, or is that it for the season?
Very often you will get new spikes coming up. These will be smaller but give colour later in the season. Often lupins are short lived perennials, lasting only one or two years. Many people treat them as biennials, removing after flowering and replace with an autumn flowering plant.
I have a couple of the dead stalks with 1-2" pods coming off them - leave or remove?
Cut the dead stalks off as described above