My title sounds like a musical so I will try not to sing as I type.  There in no BS to this title.  I have three cats here at my shop with two 5 month olds who have to investigate every new thing including placed objects, smells, and fresh fiberglass body putty spread on a steel roof.  It is safe to say I had to sand out a few foot prints from some of my patching materials.  So here we go.  I removed the remainder of the factory vinyl top from this car.  It had small bubbling from underneath from trapped moisture common to vinyl tops.  Wherever there was a small bump, that small bump was a small pile of rust power from the metal beneath.  So out comes a sqaghetti wheel to lightly grind off all the glue and minor rust.  Once that was completed I ran a stronger wire wheel on a high speed grinder to get in as deep as I could in the rusted spots.  Some spots turned into small holes.  In a perfect world I would have treated this problem from the underside but taking down the headliner is not a practical option.  These are not fun to install at the best of times.  My headliner had a couple of small mouse holes that I can patch.  After I cleaned all the spots,and there were many, I treated them with a product called Rust Mort.  I only did half of the roof with this and the other half with a spray that I have used in the past that converts rust in to an inert material.  The rust mort is a pain to work with.  You try to keep it wet for the first half an hour and then the next day you deal with the next step.  Now the product recommends a water wash on the rust mort surface to neutralize it.  It leaves crystals as it dries and drips down the roof and unfortunately down onto fresh body work.  I am not keen on putting water onto bare steel.  It seems counter productive.  I dried off the roof and sprayed window cleaner to clean anything else off before my next step.  I decided to use JB weld paste to fill the holes and also to give a thin skin over the rest of the surface defects due to the rust.  I had to do a couple of treatments to the places where there were holes as it drips into the roof underside.  Once the JB weld had dried I applied a thin coat of fiberglass body fill and sanded with a block.  The next step will be to apply body putty over the roof to smooth over any low spots that might show up even with the bed liner coating that I am planning to spray to emulate a vinyl roof.  This step wll be the last body part that I will spray on this car.  The car will be entirely painted and assembled when this occurs.  Note:  there are many ways to attack this rust issue in a pragmatic way.  I am not restoring an actual Eliminator Cougar worth well over $100,000 so putting a new roof on because of rust spots is not an option.   In the past I have used metal glue and glued small patches over the holes but that still leaves the bunch of other areas with light surface corrosion that has left rough low spots on the roof.  Body work is still necessary after this step of gluing and I don’t see the advantage of a piece of steel versus JB weld.  I feel that the JB weld will have the ability to drip down into the hole and form a bond around the underside of the roof.  It just may drip down onto the headliner which will never bee seen.  Decisions, decisions!  Keep it simple.  If I am wrong and the rust comes back with a vengeance, it will have to push through the JB weld, the fiberglass filler, the body filler, epoxy priver and finally the bumpy bed liner surface.  How many years will that take?  I can always grind down any problem areas and re spray the bed liner if necessary but I doubt it will come back.  I will put a couple of photos of the roof of my Comet that I did a couple years ago using this process.  This car had no vinyl top originally but I wanted one.  There were dents on the front of the roof skin that needed filling and blocking.  I alway put fiberglass reinforcement on the bare steel first before the regular body putty.