I have a 2004 Dale Earnhardt edition 3800 supercharged ss 108,800 miles with an annoying vibration at idle, when stopped at red light, and when slowly accelerating. mostly around 800-1000 rpms. Feel it through all the gears when not moving. No vibration when moving.

Car was running perfectly fine before dropping it off at local business to work on brakes and oil change. when I picked my car back up there was an awful vibration as soon as I started it up. They said it was probably carbon build up so tried seafoam. Didn't work. Then they kept on saying they were getting a misfire in cylinders 4 & 6 when hooked up to code scanner. so replaced all plugs and wires. Problem still continued.

Took car to another mechanic who said engine was running smooth and it was the torque converter going bad. Had them replace the tranny with a new Jasper tranny but problem is still there! this really getting frustrating. Please help! Idk what they did to my car! Really hope they didn't cause internal damage.

 

I would first probably visually inspect the motor mounts, usually something internally wrong with the engine won't cause the vibration without making some sort of a knocking noise. Also check the transmission mounts, but if you had a new tranny put in they probably would have advised you that it needed to be replaced.
You replaced the plugs and wires, there is a chance it could be the coils need replacing, or the ground on the bottom of the coil pack is not making good contact, and sadly also the slim chance you got a bum spark plug wire, this does happen periodically from time to time, you could start the car and use a water sprayer to spray a light mist over the wires individually to see if getting one of them wet cause the engine to misfire? also visually inspecting them at night will let you see if they are arcing out.
There is also the chance that you are not getting enough fuel through the system, you can pressure test the fuel system at a shop and you will find out if it's low which would be causing the stuttering, but doubt it would only cause a vibration at idle and low speeds.