Recently my 1999 ES300 has been having so many problems. It has 255,000 miles on it.
What I have replaced: New transmission
Throttle position sensor
Harmonic Balancer
Ignition Coil
Ball Joints, brakes, CV axle

Yesterday when I was driving, I saw the hood of my car vibrating due to the engine shaking. I was at a stoplight and as soon as I hit the gas the shaking stopped but it was a terrifying experience. Now I have a check engine light I need to get checked but I am terrified that it is something serious.
I'm worried that the car is becoming unreliable. I put in a lot of money for the new transmission so it is so disappointing that I am having engine issues. Any advice?

 

I'm guessing you are having some misfires. Get your codes read. Don't panic until you see the codes. Could be something simple. You don't know until the codes are read.