2003 Civic Electrical problem--It Starts...sometimes

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-Car is a 2003 Civic LX
-Just Swaped to a 2001 SI Vtec Engine (Complete D17 not just the head)
-2002 JDM Wiring Harness
-2003 SI Computer (Reflashed at Reputable Honda Dealer)
-Stereo Was just completely rewired
-A sensor needs to be rewired, bad Air/fuel
-I've had a compustar alarm for a long time


My car wont start...sometimes. Today was the second day in a row it's happened, and I don't know why.

What's happening;
-It turns over, fast, and I have 12.5 volts.
-Sometimes, The spedometer fluctuates up to speeds of 50 mph (only when it's not starting)
-The imobilizer clicks
-the stereo has also been having a lot of feed lately, which is NOT caused by the RCA's...but I just had it rewired, so who knows if this is even related?
-I usually have a check engine because of the faulty 02 sensor, but the code doesn't come up under a scan (only when this problem occurs).

What I know;
-Not a fuel issue, fuel pump is working fine
-I unplugged my stereo headunit completely (it's a double din dvd) and it didn't fix anything
-Tried plugging in the old LX computer, didn't work
-Tried swearing at the car, didn't work.

So? Something must be shorting...but I dont know where to begin. So many new parts, so many new wires....Anybody have any ideas?

The guy who did the install came over yesterday, started checking some things, played with some wires, then it started. Worked all of last night, then this morning;

Nada. It still turns over, but will never start.

Any input is appreciated.
Just found out how to start it today.

I have to plug in my OBD2 scanner, hit the "erase" button (even thought it displays there are 0 codes) and then it starts.

What's up with that?