Ok, here is my question.... If the electric trunk didn't work, and you say the trunk key cylinder doesn't either, then how did you remove it???? I know you state it never worked, how did you open it to install the power set up? Has the lock cylinder been just laying in there for show?
That being asked, if the cylinder is out, and it worked before the electric unit was installed, then most likely the tumblers are stuck/ frozen. I would soak it in a penatrating oil and a couple of jolts/whacks to try and loosen the insides up.
You could change the door locks and trunk lock with a new set and have one key for them and one for the ignition.