I just replaced the engine in my sons 94 EX (VTEC). It had a slight head leak & he forgot to check the water & roached the engine. put in a 125k mile engine. Seems to run good, but on my test drive, the D4 started flashing I checked the code & the TCU (D4) flashed with 1 & 2.
I could not find TCU code 12 in the service manual or anywhere online.
Was pretty sure I connected everything properly. Will double check tomorrow when I get the time.

 

Code 1 and 2 are for the Lockup solenoids. Verify the connections are clean and tight, look for any wire damage or corrosion on the connector.

Verify all your grounds are reattached.
You can test the solenoids electrically by unhooking the connectors and supplying 12V from teh battery directly. They should click. If not there may be a fault with the solenoid. If they do click, check the wire harness and connectors.