If you have assigned control points between the upper row images and the lower row images, there's no reason why they should not get aligned when you run the optimizer. Since you used a panorama head, make good use of the knowledge that you have concerning the angles of yaw, pitch and roll. All the images in the bottom row were shot at the same angles of pitch and roll. Likewise for the top row. The images in the same columns share the same yaw value. If you set all these known nominal values in the Image Parameters tab, the Panorama Editor window will already show a reasonably well aligned panorama. Set lens parameter values on the Lens Details tab if available.
Then (with control points assigned) start the optimization process in Advanced mode by optimizing y,p,r on all the images in the bottom row, with only those images checked in the "Use control points of" list, and with the link pitch and roll boxes checked.
Then uncheck the link boxes, and reopimize (including the lens parameters if you didn't enter a good set above. Uncheck the y,p,r boxes for the bottom row and check the y,p,r boxes for the top row. Check all images in the "Use control points of list". Optimize the top row into alignment with the bottom (fixed) row.
Centre the panorama horizontally. Inspect the y,p,r values of the immediate neighbours to the orphan image, and estimate what its y,p,r values would be expected to be - i.e. the pitch and roll will be similar to all the other images in the top row. The yaw will be the same as the image below it. Set those values in the Image Parameters tab and that should be that.