The car is a 1986, the replacement engine is a 1996 with an OBDII ECM.
This car had an electrical fire on the drivers side of the vehicle.  I hope the guy got out alright.

The cause was a hole rusted in the bottom of the windshield waterway.  The fusebox on this car is under the dashboard and the power routes from the battery to the fuse box.  The water infiltrated the firewall penetration causing a short.  The burning wires ingnited the fuel lines and that was that. 

The new harness has the fuse box mounted in the engine compartment.  Battery power goes three places: the alternator, the starter and the fuse box and is on the opposite side of the engine from the fuel lines now. 

I suspended the engine wiring harness from the overhead to keep the octopus factor down.  This was all for not because I didn't use the OBDII system.  You can see why in these two pictures.  On the right Complete DFI harness.  On left ODBII octopus. 
 ECM Part number OEM;   16214399 
This is the layout I ended up with.  The Ignition Feeds remaining fuses under dashboard.
Cleaned up the battery wires.  The OBDII wiring harness is installed here.  I later decided to put in an ACCEL DFI system and I trashed the OBDII.
This firewall penetration is the AC power and Heater fan wiring.