I noticed that the 30 Amp engine fuse was blown, so I replaced it and hoped that it would clear, but it did not.
Do you mean the 30 amp "motor" fuse? The 30 amp motor fuse is the fuse for the shift motor circuit. Code 12 is the ECU motor drive circuit which is the same circuit the blown fuse is in. If you did all the associated tests as described in the service manual and everything checks out good, you may have a bad ECU.
I then tried to clear the code, but it does not seem like pressing the up and down buttons do anything for clearing the code. All I did was press both of then together but never got the clear code, am I doing something wrong?
Did you press both of them at the same time, for more than 3 seconds, while the code was being flashed on the gear position indicator? In other words, you have to retrieve the code and while it's still flashing on the gear position indicator, push both buttons and hold them for more than 3 seconds. At this point, if the code is erased, the blink should change to the conformation code as shown in the service manual.
I really do not want to replace the ecm, but if I have to I will.
Yes, I can understand that. If you did the tests in the service manual and they all checked out good, it seems to be indicating a bad ECU. Unfortunately, I've seen the codes and test procedures indicate the problem as the ECU before and the ECU not be the problem. The fact that the fuse was blown in that circuit (code 12) would leave me to believe that the problem is in the ECU motor driver circuit, which would include the ECU, the shift motor and the related wiring. Since you did the tests in the service manual for that circuit, that seems to only leave the ECU. I wish I could help you more, but I'm just not that familiar with the Hondamatic ESP.