I briefly looked but didn't see anything irregular above the wheels, I'll check again.

I have a new ignition switch which is alarm free, it's what I've been using for all these tests.

 

Body harness above the wheels looks fine.

 

Unplugged the ignition switch and test the car side of the plug. 3/5 of the wires go to ground:

Blue (accessory)
Black/ red (ignition coil)
Black/ yellow (ECU)

Anybody go an idea?

 

We cut the wire that goes to the ignition coil (which I no longer have since my SR swap) and things are better now, but now my fuel pump isn't turning on...

 

Headlights are fine, ECU on the fritz, and slow cranking from the starter? Sounds exactly like the main ground cable from the chassis to engine has come undone or is loose. Headlights don't return power through there. The ECU's ground is directly to the engine, which explains the running issue. Your ECU controlled relays will buzz because the ECU can't hold them to ground. The ground cable is the return from the starter, and if forced to use the other tiny grounds, will turn slowly.

 

The starter only cranked slowly the first night. Now right now the the starter is cranking fine but I don't have fuel.

 

So the fuel pump fuse is not getting power. Reconnect the wire I snipped and the EGI (ECCS) relay starts buzzing...not sure if the fuel pump fuse is getting power because I don't want to set my car on fire. Who wants a tasty blue moon with a slice of orange garnish?

 

The black and yellow wire that goes to the starter, I follow it back to the fuse box, it comes out on the other side paired with a big white wire, goes into a plug, and on the other side the two wires are wrapped together and taped off. Where are they SUPPOSED to go? I'm assuming a clutch interlock relay or something? Anyone know?

 

the big white wire should go to the alt. are you talking about the 2 wires coming out of the front of the fuse box towards the battery tray? they should go to the positive plug on the battery. post up a picture of the 2 wires and lower harness if you can.