** NOTE , you will not need to remove the factory rails until all the welding is done, they can be completey removed or just section were you add the tubs.
The only place of interferance is the trunk floor, when installing the new S&W frame rails inside of the factory rail position they would need to pass threw the bottom of the trunk floor.
The best way is to remove the entire recessed trunk floor , just cut around the top , when removed it will look like this.
(This is the part that can be purchased from many of the classic parts houses.)
It is easiest to do this first ( cut out the trunk floor) then weld in the new rails butted up against the old frame rails. ( at the front and against the rear panel at the back of the trunk) Next cut out a narrow section down the center of the removed trunk floor and weld it back together forming a new narrow " mini trunk floor". When reistalled you will have to weld in a flat peice on either side to compensate for the narrrowed trunk floor and it will look stock.
If you use ladder bars you will have to fabricate an upper shock mounts. If you use leaf springs I would suggest sliders in the rear to replace shackles. You may want to move the axle back an inch to give you more clearance athe front of the wheel well lip to help clear tall tires.
This is my 65 with leafs and sliders. With the rails welded just inboard of the factory rail 12" tires are no problem, It gives me about 16" between rails and the wheel well lip.