A/T. Where is shift solenoid A?

Wow, often people have no clues or details as to what is wrong....well you sir win the "covered all my bases" medal as far as I am concerned.....Sorry I can't help.

It sounds like you have a Bad Shift Solenoid that is shorting out, Cleaning the Solenoid probably moved the "WIRE" and then when reinstalled, worked it way back. If the Shorting of the Shift Solenoid causes the issue with the PCM/TCM, then either your PCM did not have an issue or the Solenoid just took out your new PCM due to not repairing the issue the first time. I personally would start out with changing the Solenoids (ALL OF THEM) and Un-Plugging the PCM while doing the repair. This will do a reset for you.

Usually it means the speed sensor in the transmission is failing.
The blinking light means your overdrive may not work.

D4 light flashing indicates a problem with the transmission. Need to pull trouble code from transmission control unit to find out what is wrong. most likely it is a shift solenoid going bad.

Flashing D4 light is an error from the TCU (transmission control unit), so you got something going on with your transmission. If you want to pull the error code, remove the passengers side kick panel and look for a pair of wires with a blue connector at the end. Stick a paper clip or some other piece of wire into each hole of the connector to short the wires. Put your key in the ignition and turn 2 clicks. The D4 light will flash the code...short flashes=1 and long flashes=10. Add the number of short and long flashes to get your code. Errors are below:

0-Transmission control unit (TCU) faulty.
1-Lock-up solenoid 'A' circuit open or shorted.
2-Lock-up solenoid 'B' circuit open or shorted.
3-Throttle Position Sensor circuit open or shorted.
4-Vehicle Speed Sensor open or shorted - No signal from speedometer.
5-Shift Lever Position Switch circuit shorted.
6-Shift Lever Position Switch circuit open.
7-Shift Solenoid 'A' circuit open or shorted.
8-Shift Solenoid 'B' circuit open or shorted.
9-Counter shaft or transmission speed pulse generator open or shorted.
10-Coolant Temperature Sensor open or shorted.
11-Engine RPM (Ignition coil signal) open or shorted.
12-(No code 12 used)
13-Main shaft speed pulse generator open or shorted.
14-Linear (line pressure control) solenoid open or shorted.
15-Kick down switch circuit shorted.

there are solenoid on the transmission, you can take them out and clean the screen then change the transmission fluid.

This is involved. When the D4 light blinks, it is indicating a problem with the input or output systems for the A/T. If you find your Service Check Connector (it should be near or at the top of the kick panel on the passenger's side; it's usually blue and has two holes in it; it is at the end of a wire so don't look for a fixed unit; it is often simply tucked in behind the top of the kick panel. You should pull the kick panel out to find it) you can insert a paper clip so that it connects the two holes. Then, if you turn your ignition to ON II (do not start the car) the D4 light will blink out a code, using both long and short blinks. The blinks have to be carefully counted. Problem codes 1 through 9 care indicated by short blinks. Problem codes 10 through 15 are indicated by a series of long and short blinks (you have to add them together to get the code).

I tell you all this to indicate that the procedure is fairly involved, and since you probably don't have a list of what the codes mean, I would have to say that it would be best to find, if you can, a Honda dealer to read the codes and check your transmission. Most of these problems are connector or sensor related and are usually indicated by the transmission not shifting from one gear to another, or by the transmission jerking hard when it shifts. If your having no problems and you are in a position to not have access to a Honda service department, you can find the backup radio fuse in your engine compartment fuse box and take it out(not with the car running) for 10 seconds or so, then put it back. It will clear the computer. If the D4 starts blinking again, it would indicate that the warning was not just a glitch.
I really hope that this is helpful; I'm sorry if it is only disheartening.

you have a transmission fault the D4 light blinks to tell you that there is a transmission problem when the light is blinking the transmission computer put the transmission into limp home mode so it will not shift normally and you should try not to drive it very far when it gets to this stage you need to have the transmission codes check to pin point the problem

this indicate a transm. failure, begin to check fluid transm. level.

If the S light is blinking, this indicates that there is an electrical problem somewhere it the TCM circuit. I have included a link that takes you to an excellent page which shows you how to read the codes and what they mean.
http://home.earthlink.net/~michaelpkeefe/HowTo_Codes.htm
Also, The top solenoids are for the lockup clutch and the bottom ones are the shift solenoids.
As for the Immobilizer causing problems, if it was incorrectly wired to the TCM, then it could possibly cause a problem.