I am in the middle of doing something similar on my '89 FJ62. The truck spent some of its life in Ontario so the rocker panels, rear fenders, and quarter panels were all in terrible shape. There was actually mud sprayed up on the inside of the passenger-rear window because everything was rusted away so bad! I ended up buying the Wolf Steel replacement panels and doglegs, because I didn't think it was worth it to try and fix or cover the problem areas with fiberglass or bondo. I'd rather just cut the majority of it off, and then start over with something new...even if you're only keeping it for a few years, at least it looks nice while you own it, and isn't a turn-off to whoever is looking to buy it from you in the future.
I ended up taking a zip disc and trimming about 2" off of the outside edge of my inner fenders because it was all jagged and rusty, which means that there is now a 2" gap between the inner guard and the outer skin...obviously needs to be sealed up with something to prevent moisture and crud buildup inside the new panels. On the dogleg part of it, I just opened the door and then cut some chicken-wire to an approximate size and stuffed it in between the dogleg and the inner fender (the dogleg I had riveted on with some small brackets I custom made out of some scrap metal) , then laid fiberglass over top and around the outer edge of the dogleg. Worked really nicely there. The next step of the process is to seal that 2" gap off from the inside of the fender which is much harder because you are working against gravity. I tried this today and was only parially successful. The other thing I was originally going to try was to take some of that flexible plastic garden edging and just rivet it to the inner guard and the outer skin, but I couldn't figure out a way to make it work nicely.