I've just restored my 1978 40 and used the aluminum fenders both sides. If you have the money and want to do the work yourself it is amazingly easy to replace the fenders, just unbolt old and bolt in new. If you are going to have someone do the work on the old fenders it might be cost effective to put on new aluminum yourself. They would not have to be painted, but you can paint them putting on a coat of etch primer and then painting with color over that. The aluminum fenders have slightly different form than original but they should last forever. My picture shows the results of installing an aluminum tub aft and the two front fenders. I purchased my aluminum fenders from JTOutfitters www.jtoutfitters.com/ but they are available from many FJ40 parts suppliers.
I'd replace that first one. Maybe try and salvage the other. I'd check under the front turn signals too, most cruisers rust there first because of the welds on the signal bracket. You could have a body shop paint it to match while it is off your cruiser and install it yourself. You can look around for used one, but be careful, you may get one just like yours covered with bondo and paint.