Rep Power: 0

I have a 1997 civic lx that's all stock. When I start the car it shakes like it is going to die, and it idles at a low rpm for like 3 seconds. It then goes up and the shaking stops. It doesn't shake while driving. Only when starting up. It is worse in the morning. Sometimes later on the day it starts normal. I haven't done any major repairs lately that could have caused this.

 
Rep Power: 0

This may sound weird (this happened to me so maybe its happening to you) bubt it could be the starter. The starter is supposed to kick the engine into a high enough RPM, so maybe its just barely getting enough RPMs to start and the engine has to do the rest of the work thats where the shake is coming from.

i know it sounds weird, but i had that problem right before my starter went out. I replaced it, and works like a charm.