Why would you try and even use the 07 harness at all? Take everything out of your 04 and swap it part for part with the 07. It’s a PITA but it will work. The beds are interchangeable from 02-08. I have an 05 and put an 08 on due to the rust I had.

 

Ok, bear with me, I'm about to drop alot of info on you.

Frame:
3rd gens have a tube type frame. Painting the outside is good, but you have to do something about protecting the inside. Industry product term for protecting the inside is generally cavity wax. There are a few products out there that are effective. The 3M stuff is pretty good, but expensive. Eastwood is similar. Then there are the lanolin based products, Fluid Film, WoolWax, and Surface Shield (from the pbBlaster guys).

POR, Chassis Saver, and KBS are all similar "moisture cured" paint. They tend to be durable only if applied properly and maintained. Plan on keeping an eye out for any peeling, because if they do - it'll come off in sheets. I've used POR15, but I like Chassis Saver, because its available off the shelf in a couple local to me stores and its affordable ($30 a quart). All of them break down with UV, you need to topcoat them if exposed to direct sunlight. And they all SUCK when it comes to application. It'll stick to your hands for days - wear disposable gloves. If brushed, I just buy cheap brushes and toss them when done. I have a $10 Harbor Freight spray gun when I spray Chassis saver, and I use about 10% of their reducer - otherwise it'll have small bubbles when it dries. Clean your spray gun immediately when you apply each coat with lacquer thinner - else toss that cheap $10 gun. For best results, you need to put on multiple coats, and the wait time between coats is long (4 hours or more). Read the directions. I'm well practiced on Chassis Saver and I haven't used the POR product for close to 20 years now. Never used KBS, my friends seem to prefer it but I don't know if its any better. I find its much faster to spray epoxy primer and topcoat with urethane for a durable coating, but if you're painting over rust, use the moisture cured paint.

Body:
There are two issues when it comes to rust. Exterior paint integrity, and inner cavity moisture. Exterior is easy, keep it clean and repair any areas where the paint gets damaged. Most everyone gets the obvious salt treated road effects of the Rust Belt. Less understand about condensation effects when the temperature changes. Everywhere two panels are tight or close, tends to hold condensation much longer, and that moisture (along with the dust/dirt that starts sticking to the surface) eventually breaks down the factory cavity coating and rust starts to form. Cavity wax is a good preventative, but its not a one and done process. If you do a really good job, probably can maintain it with another quick spray every other year.

So while you have the body separated from the frame, I'd inspect it well and repair any areas where you have coating failures. Lots of horror stories about coatings that harden (like when moisture gets under them. Spray the inside with the cavity wax you like best.

Specific areas... the cab has some access points on the back side of the rockers covered with black tape. Rip that tape off and go in there with your cavity wax applicator, and make sure the rocker weep holes are open and clean. Then get some replacement tape and close it back up. Take the interior panels off the doors and spray cavity wax in the bottoms and make sure all the weep holes are open and clean. The bed.... 3 spots you need to look at. Lower sides near the cab, there is a reinforcement panel - clean then cavity wax the area between and around the bed side and reinforcement panel. Lower sides near the bumper, there is another reinforcement panel that needs to be cleans then cavity waxed. Lastly, the dreaded wheel opening. Harborfrieght has a long extension for your air gun (I'm assuming you have a compressor) that makes cleaning out the wheel opening easier. Take out the tail lights, then direct the compressed air at the area between the bed side and outer wheel house. Clean it the best you can, then fill it up with cavity wax. Tailgate - get cavity wax inside the lower half it.

Cavity wax - most likely, if you're just spraying cavities, you can get away with spray cans and the 36" extension wand. If you want to just generally spray the lanolin products it all over the underbody, I'd recommend the kelsport gun setup for about $100 and buy the gallon can. HomeDepot has Surface Shield spray cans (but you'll need an adapter for the wand). HomeDepot has fluid film cans, as does AdvanceAuto and other autoparts stores. AdvanceAuto generally has the gallon fluid film, and it can be picked up on amazon as well. 3M products are available online and at your local autobody supply stores.

Here are some links (some seem to not work as links, copy and paste them):
https://www.kbs-coatings.com/

https://www.magnetpaints.com/underbody.asp

https://www.fluid-film.com/

https://www.3m.com/3M/en_US/collision-repair-us/featured-products/cavity-wax-plus/

https://blasterproducts.com/product/surface-shield/

https://www.kellsportproducts.com/Extension-Wand-fits-Woolwax%C2%AE-AS12-Aerosol-Cans-24-or-36_p_32.html

https://www.kellsportproducts.com/Woolwax%C2%AE-Pro-Undercoating-Gun_p_16.html

 

I spray the lanolin products under my mowers - grass clipping don't stick anymore. But I don't use spray cans, I use the kellsport gun and bulk lanolin (usually fluid film cause its easy to acquire).