I pull my boat with a van. The lights come out the back door of the van. The wire harness is pinched between the back door and the back of the van, and it's causing my trailer lights to short out. In other words, I am basically lightly shut the door on the wires, but that's ruining them.

 

My first problem will be solving this, so it doesn't short out. But before I do that, any recommendations on how to prevent the wires from getting pinched, or this will just keep happening after I fix it.

Drill a small hole in the floor inside near the door. Fish the wires through the hole and protect them with a rubber grommet. Secure the wire harness to the van near the trailer hitch. 

 

 

 

No 3 pin connection in back of van ❓

If not, I'd wire one or have it wired.

"Normally" the factory wiring runs down the frame and up into the vehicle in one corner of the rear and then over to the other side.   You just splice into the factory wiring coming from the front because it has the wires for both sides.  However, with that said, I seem to remember having to go inside on the left side of a friends Ford Van to plug in the adapter and then run the trailer light pig tail through the bottom and over to the hitch.  That required drilling a hole, installing a rubber gromet and sealing it with RTV.

I would do whatever it takes to keep from going out the door with it.  

Best DIY is @Dogface solution or @Bird is the answer. U-Haul will wire in a flat plug very inexpensively, which would be the ideal fix.

If you can find an adapter kit for your model van, that would be the easiest way to go as long as it doesn't go out the door. Get one that exits from the chassis and to be extra proactive, consider a sleeving (braided cover) to protect the wires if they don't already have it. 

Sleeving

Some other items to consider:

Use a self fusing silicone tape around the connectors to protect from the elements.

Use a dielectric grease on all connections to further prevent corrosion. 

These plug in adapters are the more expensive option but they are the quickest to install. This one is made by Hopkins.

 

Those adapters are not optional on vehicles that have a separate turn signal bulb from the brake/taillight.  They are a must have unless you know how to use diodes to isolate them and make your own (like I do).  They are a MUST HAVE, or you will never get you trailer lights to work properly and to keep from blowing fuses.  You buy them made for the vehicle you are installing them on and just unplug the existing connecter and plug the adapter in.  If the connector is inside the vehicle you will have to drill a hole to get the trailer light pigtail out to the hitch.