As the Title Says 99 through 01 ZF-6 Swaps are not the same as 02 and 03 when it comes to the wiring!
If you are reading this and was like me, you just got done swapping all the hardware over and realize that the other threads with 99 model truck's wiring isn't matching up to your 02 or 03. Don't worry, it is possible, just a little more complicated. My truck is an 02 and is now successfully swapped over and functioning as it would have if it had come from the factory with the 6 speed. And for the record, I love it. It was a MAJOR PITA for me figuring everything out, but I'm going to try and simplify the process in this thread.
1st of all, the Mechanical process of the swap is the same. I had no problems with making everything work and it has been covered plenty of times so I'm just going to focus on the wiring for the 02-03's. I have right at $3,000 in my swap and that’s with a $700 Valair Clutch.
First, you will either need a Chip reburned for a manual transmission or a manual PCM. I tried the Chip first and the truck ran, but I didn't like the power I was getting. Its seemed like my chip was stuck in 60 horse position and wouldn't go any higher. Possibly because the tunes were wrote for a different HEX code, but I don't really know. I picked up a used pcm for $260 through Car-part.com.
Where Our trucks are different from the 99-01's is that we can't trade pcm's like baseball cards. I got a 2C3F-BE with a HEX Code of AEB4 for a 2002 or 2003 F250 or F350. The 2C3F will be the same but the suffix BE will change. The BE is the standard emissions non California, non Cold weather. I would suggest this one only because I know it works. I'm not sure about the others.
There are a couple different phases to the wiring, the first being getting the truck to run.
For a Temporary Fix to get the truck to turn over and crank you need to connect the Tan/Red and the White/Pink wire together at the automatic transmission's Range sensor. This is the connector where the Shifter cable connects to the auto transmission.
Now it will crank and run, HOWEVER, you will throw a PO118 Overheat code, the truck will run like crap and you'll get terrible fuel mileage. Here's how to fix it:
The Manual transmission PCM is looking for an additional coolant temperature input. This happens to be the Orange/Black wire that goes to the transmission temperature sensor. You need to purchase a additional coolant temp sensor and pigtail from Ford. The Sensor is P/N F5AZ12A648AB. You will need the pigtail to fit it, but I'm not sure what the p/n is on it.
You can install the additional sensor in the test plug on the side of the thermostat housing, or if you have a Coolant Filter like I do, you can put it into one of its ports. Just so you know, in my set up it does throw a soft code because the two sensors are not reading very similar temps because the 2nd sensor is away from the motor and a bit cooler. I'm not worried about it at this point.
For wiring the 2nd sensor in you need to "T" into the Gray/Red wire on the existing Coolant sensor and run it to the same side of the new sensor. This is the Universal "power" wire for all the sensors. The other wire of the new sensor will go to the Drivers side wheel well next to the pcm. Looking down into the corner next to the cab on the Driver’s side you will see several connectors going down to the transmission. There should be a black one on top and a gray underneath it. The gray connector is where all the action will take place. In the pictures the black one is disconnected so it will be easier to get to the gray connector.
On the gray connector you are looking for an Orange/Black wire. Cut this wire on the transmission side of the connector and connect it so that it is running back through the connector and into the pcm.
The second Picture is backed off for orientation.
This will get the truck running with no Hard Codes. However your Clutch pedal position switch and cruise control won't work…. More wiring for that.
I'm out of time now but will try to finish it tonight.