How should I go about fixing this rust?

And did you coat the new metal in anything to prevent further rust
I painted the new metal with Tremclad enamel and applied Dominion Seam Sealer to all of the joints. I then rattle can sprayed on Dominion Sure Seal undercoating. The final step was to shoot Krown T-40 rustproofing into the torque box with a Shutz gun.
 
Yeah I need to look
I painted the new metal with Tremclad enamel and applied Dominion Seam Sealer to all of the joints. I then rattle can sprayed on Dominion Sure Seal undercoating. The final step was to shoot Krown T-40 rustproofing into the torque box with a Shutz gun.
into doing this because my torque box on my drivers side is rusting pretty bad.
 
Having done both torque boxes on mine, I can tell you it's not exactly a cake walk. And you have to brace the tub somehow while they are out so it doesn't warp.
 
Not sure if it's been said but take a good look at your torque boxes. Patch panels are available but you might be looking at full replacement.
Due to the extreme difference in the amount of work to change out a complete torque box, I opted for Safe-T-Caps for mine. Depending on what the OP discovers with his torque boxes, they might be a more viable option (read that as "a helluva lot less work and money"). For mine, all the rust was confined to right at the body mount locations. I couldn't actually see any rust, but the sides of the torque boxes were bulging outward slightly, being compressed right at the body mounts. Thorough investigation showed the true extent of what I couldn't see...
img_0794-jpg.jpg

One way to get an idea of if you have rust issues in those areas is to try and remove the body mount bolts. If any of 'em just spin, then the nutsert has likely lost its grip due to rust. That's been my experience, anyway.
 
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I went to a body shop I’m my area and he said with the labor part not including the price of the part it would be around $700 to replace the quarter panel and make it look oem.
 
Here is what I am talking about. On my TJ you can see the "rust boxes" that are behind where you see rust breaking through on your TJ. Water and stuff gets in between at the red arrows. And also inside those boxes and you can see the blue arrow I have some rust coming through from where water/mud had collected inside the box.

View attachment 128922
Where did you drill the holes?
 
I painted the new metal with Tremclad enamel and applied Dominion Seam Sealer to all of the joints. I then rattle can sprayed on Dominion Sure Seal undercoating. The final step was to shoot Krown T-40 rustproofing into the torque box with a Shutz gun.
Sorry it’s been awhile but I’m thinking about getting those torque boxes fixed along with the rust in the back of my Jeep, but I was wondering do you think a body shop would do what you’ve done to your Jeep to mine without costing me 5 grand?
 
So I went to the body shop and the guy told me that he couldn’t find the pet but I looked at Quadratec and I think this is the part is this what I would need? https://www.quadratec.com/products/22505_0009_07.htm

That's the part you will need to fix the body exterior but you may find problems in behind it.

EDIT: - Sorry, I see from another post above that you got an estimate of $700 to replace that panel. That's seems pretty good. Does it include paint?
 
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Sorry it’s been awhile but I’m thinking about getting those torque boxes fixed along with the rust in the back of my Jeep, but I was wondering do you think a body shop would do what you’ve done to your Jeep to mine without costing me 5 grand?

I can't say what it would cost but I think a shop could give you an estimate. They would likely qualify it by saying they can't be certain until they dig deeper, for example in behind the part you mentioned above. You're probably looking at a specialist vs. a shop that does collision work.
 
That's the part you will need to fix the body exterior but you may find problems in behind it.

EDIT: - Sorry, I see from another post above that you got an estimate of $700 to replace that panel. That's seems pretty good. Does it include paint?
Yeah that included everything.