The new trunk was placed in, taken out, placed in, taken out, over and over again. A cut here, bend there, try the fit again. Once we looked everything over twice, maybe three times I spotted her in there. Making little spot welds held the trunk in place and I went back to weld the necessary places to cement the pieces.
Once I grinded the spots down smooth we cleaned them off and threw some primer on there. I came back the next day and found a couple other places around the butt that needed more welding that I never finished before. I'm very happy that this section of the car seems to be complete for now and we can move on from here.