Powertrain management all ECU signals showing short circuit

I bought an Audi 2004 A4 B6 avk engine V6 3.0 liter automatic Tiptronic early this year January sometime, the heads we're blown and the valves were bent after fixing the mechanical issues I put it all back together. Well putting it back together, I made a mistake and accidentally plugged the Hotwire going to the alternator to chassis ground... (main engine ground) When I went to plug the battery back in the negative terminal arced due to the alternator wiring mistake.

After fixing the wiring I was able to start the car had a leak so I shut it off. Started up again well getting up to look at the motor while it was on the engine shut off and would never start again I lost my spark and fuel command from the ECU. I've checked all the fuses a few have some shorts but all fuses are intact some of the relays are receiving shorted signals from the ECU

I ended up sending it out to a mechanic he was able to find a Arc between two wires on the crank sensor harness from the ecu. I replaced the crank sensor with a junkyard sensor tested fine. And also fixed the crank sensor wiring from the ecu and replaced the ecu

Well I finally found someone that was able to program the security information from my OEM computer and transfer it to a flashed working computer. After installing the reflashed computer the car started ran well, I was able to shut it off I then turn it on again for the second time ran well but I shut it off due to the fact that it had no coolant on the third attempt the engine would not start I got the same code a PO322 and no spark or fuel commands from the ecu

Rotatingrotor89 wrote: some of the relays are receiving shorted signals from the ECU

I'm not sure what you mean by this but when I read the heading of your post I thought "Audi"!
I had an Audi that would occasionally throw fault codes for almost everything on the engine and not start.
The only way to get it started was to disconnect the ECU for a few seconds and connect it again. Then it would drive fine for a while but suddenly
die and bring up those fault codes.
I eventually saw on a wiring diagram that all those components were fed by the same relay and fuse. I changed the relay but it happened again.
When I removed the 25 amp fuse I saw burn marks on the sides of the contacts - it had a bad connection on the fuse/holder.
I could start the engine and gently press that fuse sideways and it would die and bring up the fault codes. The fact that the voltage dropped so low
had the ECU assuming that all the components were shorting to ground.

Definitely correct for thinking Audi they have some many modules it's a tough electrical system. I've checked all the fuses I've pulled them out haven't seen any melting contacts. I noticed I have a few mini fuses and large fuses showing ground on one side of the circuit and 12v from the ignition side.

I did notice today I have a 10v short on fuse 31