Having done a Subaru wire merge, the ls wiring was actually fairly easy. The nice thing about LS2 wiring is that most of the wiring only involves a few connectors. I'm not going to focus on what wire goes where. This will vary slightly based on what LS motor you are using. If you are using an LS2 ECU then I would highly recommend Burtonocrs thread on Norotors. (http://www.norotors.com/index.php?topic=846.0) I've updated his spreadsheet with some of my notes that you can download here. For this page I'm going to focus more on connector location and give an overview to the wiring. Once you know the locations of the connectors it's a simple mapping game and figuring out the best way to route the wire. I made a YouTube video finding the connectors as well. So that may be easier to watch.
Let's start with locating the ECU location and the LS connectors that will be used. On a Pontiac GTO or Corvette the ecu is actually mounted right in the engine bay. So I decided to do that on mine. I mounted it on the passenger side below the wiper motor using 2 stainless self tapping screws.
Now the ECU has 3 connector sockets on it. 2 of them are used for the wiring that runs directly to the engine. You shouldn't really have to touch these. The 3rd one (the blue one) is the C1 connector. This is the harness wiring that would run through the firewall on a GTO/Camaro to hook up with the dash stuff. So the C1 connector you treat like a giant pig tail. Mine already had the connectors cut off the dash end. If your harness still has connectors they can be cut off. You basically want the big blue connector that plugs into the ECU, then as much wire coming off of it as possible. I fed it through the rx7 firewall using the same stock rubber grommet the rx7 wiring used. (I had saved it off the rx7 engine harness I sold) 90% of your wiring is going to be connecting the wires off of this C1 pig tail.
The 2nd LS2 connector that will be used is located just off one of the other ECU connectors that runs to the engine. It's a big white connector. The connector itself can be cut off. This pig tail ends up going down to the transmission for things like the reverse light sensors.
The final LS2 connector (Connector 5) is off the same pig tail that runs to the MAF. 12V switched power needs to be provided to some of these wires to power the MAF and o2 sensors.
There are six connectors you should locate on the Rx7 harness. Two of them I didn't really use and I'll explain why later. In the passenger kick panel you are going to find 2 connectors (X-05 and B1-20). B1-20 is used as it goes to the check engine light. It also contains a switched +12V wire that you can use as a power source. I used it to power my Digital Dakota box. X-05 has 2 of your main ignition wires that will provide provide switched power to the to the ECU.
The X14 connector is located on the firewall behind the glove box area. This is probably the most difficult connector to get to especially with the dash in. It can also be the most confusing connector. Now depending on what you saved from the rx7 engine harness you may or may not have a male connector pig tail to work with. If you do it will give you some more wire length to work with. It's confusing because the wire colors on the female side of the connector, do not match the colors on the male plug side. So when someone tells you find the blue wire on X14, you aren't sure what side they are looking at it from. This connector will also vary if the car is an automatic or manual. If it's an automatic the connector will have a few more pins. Now on the x14 connector some wires need to be grounded. Other wires need to hook up to the reverse switches. So in addition to the big C1 pigtail from the LS1 harness running through the firewall, you are going to need to pass a few wires from X14 back out the fire wall.
Now X-06 and A1-04 are located on the drivers side. These are the 2 connectors I located but didn't really use. The oil pressure gauge on the cluster runs through X-06. But that doesn't really matter as there is already an oil pressure sensor pig tail out in the engine bay. A1-04 is a 2 wire connector for the clutch switch. When the clutch pedal presses in, it completes continuity between the 2 wires. This allows the starter to engage. You really don't need to touch any of this. The starter trigger wire is already out in the engine bay.
I didn't go crazy and pull out every wire I didn't use. I didn't reroute everything either to do a wire tuck. But I was able to clean up a lot of the wiring so that the engine bay doesn't look too cluttered. I'll describe what I did below. This is the stuff I wish I had when I started.
Now x-12 is the middle grey connector on the drivers side strut tower. This wiring can be cleaned up pretty easily. Unplug the X-12 connector, and the other grey connector next to it. You should be able pull a portion of the harness right out. You'll have to remove 2 of the 10mm bolts where it goes into the power fuse block in order to free up some of the wires. That's fine. It should look like this when you are done.
Start un-taping everything and some connectors are going to fall right out. Then you'll have something that looks like this.
Now you can plug the 2 grey connectors back in. There are only 4 wires you will need here. You can see I've got them pulled off to the right. The big thick black wire with red stripe is the starter trigger wire. This needs to be ran to the starter. The brown wire with white stripe is the low coolant warning buzzer. This needs to be grounded. The black wire with white stripe is switched +12v which can go to Connector 5 on the ls2 harness. The grey with red stripe wire goes to the oil rx7 oil pressure sensor that you adapt to fit on the ls motor.
Now if you removed the ABS you are going to have some connectors over in the back left corner of the engine bay. I found that there was plenty of slack to pull the connectors out of the bay and into the fender area. There is also another wire here there runs across the engine bay all the way up front to an impact sensor next to the hood latch. I was able to unplug this and re-route the wire inside the fender to get it out of the bay. On the back drivers side there are 2 computer looking things. One is some ignition amplifier and the other is some resistor pack. Neither are needed. They can be unplugged and the pig tails pulled into the drivers side fender area.
Now the only wiring left to deal with is the front relay box. WIth my Samberg radiator setup, this was right in the way. Initially I was able to mount it upside down out of the way. But then it filled up with water on the first rain, and caused some of my relays to behave weird. I came home and my pop up headlights were going crazy. The best thing you can do here is extend the wiring so that you can mount the relay box over on the front driver side area near the fuse block.
I used a Miata battery in my rear passenger cubby to power my rx7. I made a floor for the battery out of wood. I have 0/1 gauge wire that runs up the passenger door sill, out into the fender, into the engine bay through the same whole the abs connectors pass through, and then down to the starter. I used some DEI heat shield loom where it comes close to the header. From the starter I then daisy chain it over to the alternator. Then from the alternator I daisy chain the power up to the fuse block. You should have a free spot on it after simplifying the X-12 harness up above. For the engine to be grounded properly BE SURE to run some ground cables. I ran 3 thick ground cables from my engine bay to the motor. If you forget this step you could cause serious damage (aka burn up) some of your wiring if you were to try and start the car.
EDIT: I got rid of the Stinger Circuit breaker you can see in the pics above. It gave me trouble. The car would always start hard and sometimes the car wouldn't have power even though the breaker was still flipped on. I switch to a Rockford Fosgate ANL fuse holder. The car starts so much better now.
The Samberg radiator comes with 2 SPAL fans. These need to be controlled by the LS2 ECU. The LS2 ECU has a low fan and high fan wire. Now GM did something tricky with their low/high speed wiring. A lot of manufacturers will utilize a big resistor. When the fan is on high the current bypasses the resistor. When the fan is on low, the current passes through the resistor. This is pretty common with Mitsubishi/Dodge. But GM actually uses 3 relays to force the fans to run in series on low and in parallel when on high. So to wire up the fans I bought 3 sealed relays, 3 pig tails, and 2 SPAL fan connectors.
Hopefully my wiring notes will help you. Definitely take your time and label everything first. With the DBW pedal you are going to need a pigtail for it. You'll also need to buy an odb2 connector. Before taping everything up I'd run 5 extra wires through the wire wall. That way if you ever need to wire anything up in the future, you'll have some wire there. To get the Rx7 speedo correct you'll need a Digital Dakota box. I mounted mine where the stock ECU was. To get the tach working you'll need to add a pull up resistor.