If the vertical part with the striker is bad can I drop it out and put a new one in along with the rocker channel?
Do I have to remove the bonded body panels?

If it's bad only a short distance up you could fabricate an insert, pocket weld it in, and then install the new rocker channels. Usually the replacement rocker channels come with an insert but it is quite short, you may need to duplicate it in a longer version. To answer your question I believe you will need to cut some glass to loosen the bond to the jamb piece for complete removal.

Also, it is attached to a plate that goes behind the seats that you would have to cut the welds on. If it is in that bad of shape, you may have even more hidden damage.