Take a look on my website to see how I used couple quarters on my convert. The quarter window sill is different between coup and convert so you need to save this piece too. Also, your convert probably won't have the jam vent that the hardtop does. Check these things out and then have your body man decide which is easier.

I am for keeping as much old metal as makes sense and if you've got to do a bunch of seam welding, you might as well go this route. If you really need to do the whole quarter, I'd lean toward the convert panel and graft in your old louvers.