KA24sleeper

I have recently replaced my engine mounts on my car ( ka24de) and i thought it would stop the shaking problem but it didnt it just reduced it. My tranny mounts are still orgian and blown and my engine is stock. I recently did a rebuild about 9k miles ago and did everything to spec. When i started the car fresh after the rebuild it shook and thought the mounts were bad but there not now after replacing them. I still have all original stock parts and nothing i can think of warped when building it. The only think i can think of is that the harmonic balancer is off because i took it apart to clean it. Im hoping its that. And ideas? ( note i have new injectors and timing is spot on the rebuilt is from top to bottom so every seal and bearing is new)

__________________
SUSPENSION>Power