Yikes! That's really unfortunate! Especially after you just spent a bunch of time perfecting your polishing skills on those fenders!
Have you considered buying new front fenders? They're reasonably affordable and reasonably easy to remove and replace. I realize this means painting but it's an option none the less.
The box sides are more challenging for sure... Something worth considering is finding a used box...the same color. One without the flares. You might even find fenders too!
The reason I mention these options is I'm concerned even after you repair these areas, the rust will keep on trucking and will become evident very soon. My experience is the rust you see represents only about 10% to 30% of the "affected" area.
If your set on patching, then I'd glue the new pieces in. This process is perfect for tight areas as opposed to welding because welding and grinding will make your repair area larger than you'll want I think. There's lots of adhesives on the market for a job like this (rust challenge aside).