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Hard to say honestly.
Does the idle eventually level out? does it drive smooth after its warmed up?
Couple things come to mind off the top of my head.
-Bad gasoline (cheap fuel with a high water content)
-Miss fire (usualy caused by bad plugs or wires)
-Leaking head gasket or bad head
When my 3.0 was going out I noticed it would occasionally shake violently when I started it up. Almost as tho the motor was going to jump out of the truck. It would level out once it warmed up but as time went on (over the period of the next 1000 miles) it gradually became worse and worse till one night while picking up a pizza my head gasket blew.
In this case the shaking and rough idling was caused by the engine trying to burn off the coolant that was leaking into the cylinders. You might check your coolant and oil, see if you notice any mixed together. I doubt its a transmission issue if it only happens when you start the vehicle. If it still drives properly without slipping and all your gears are working I would look closer at the engine.
If you are getting a check engine light try to grab the codes its throwing and post them up here.
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