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Did you use any tools to pull the old one up? Did you just use force? Where did you pull from ... the middle? the end?
Thanks,
Alex
First, push the seats all the way back, then just apply some force and pull the door sills upward. The sills are hold by couple plastic clips and they're pretty easy to pop out.
When you done, just tap the new sills down a little bit and every is back to normal, except you'll get a nice blue Lexus sign on your door.