Worked on getting some of the cancerous metal out from around the wheel well on the drivers side in the back. Going to pick up some metal tomorrow and finish cutting the bad metal out and get the hole patched up. Not really concerned with how it looks just want it sealed up.

So is pop riveting and then sealing the cracks around the new metal with fiberglass about the easiest way to get this done?

You Could, but you have some hard curve lines to follow.

From your pix, I would get a piece if at least 18 ga. flat sheet,
 cut it to a little larger than the opening your have made.
Then with a wire welder, tach weld it in place. This way your can
follow that wheel well curve nicely to give it strength again.

See if one of your Rusty Iron Buddies has even one of those 110 AC  wire (flux core) welders.
They "Spatter" alot, but they work for these kind of repairs.

CAPT

Ok so next step. I need to get the piece off that holds the stock fender flare on. That piece itself is sold but the quarter panel behind it is totally wasted. Is this thing just spot welded on? I would really like to keep the stock flare for not. I looked at maybe doing bushwhackers. However, I have much more important things to spend money on besides 450 bucks for some plastic fender flares.

This photo shows a "Spot Repair"
Again, cut out the rust, and you can Tack Weld a small repair piece in, finish off with fiberglass or thin coat of filler.

Next, The flare brkt, drill out the spot welds, clean up the rust behind it,
Drill new holes to "Pop Rivit" it back on & you can use the OEM flares.

Hope it gives you some ideas,

CAPT