Daze may be around still today to answer but I installed them on mine.  For the front, I installed them against the bottom of the frame extension.  I think the installation shows them welded through the sides but the bottom of the connector goes against the bottom of the extension.

In back, I ran into what you are experiencing and nearly all connectors will have the same issue.  Since my floors were out for rust repair, I removed the lowered portion of the floor that interfered with the connector and covered the area with a flat piece of sheet metal.  I think if you "motivate" the connectors into position on your car you won't find that the floor is terribly distorted.  On the 66 there is a screw-in plug/plate and I think one of those screws may have sat on top of the connector and if that is the case on your car, I would suggest you remove the screw and perhaps rtv the plug.  The area of the plug is punched and the radius sticks well below the floor.  If you remove the plug you can probably fold the radiused area up to lessen the impact on the floor.  You want the connector to fit firmly against the frame rail in back so some gentle persuation of the floor will be required.  If you attempt to space it away from the frame you will lose the strength in the joint you are trying to gain.   I don't have time for pictures right now but my car is still on the rotisserie if you need any additional pictures.  I have the floors in now so the area is pretty clear to see.