I changed a wire on my engine and machined my rotors.

Now my car doesn't shake as much, but it still shakes a little when in drive with the brake pressed. Is the shaking a given since it has 135k miles?

The acceleration is better but it still jerks a little but now it also jerks when deccelerating. What could be the problem?

Both problems seem to be worse when the AC is on... Does that mean anything?

Oh yeah, I have a rust hole just a little below the left side window, is there any quick way to patch it up?

 

One more thing, when I turn the wheel, I sometimes hear a clicking type noise, what could be causing that?

 

A new axle would probably be the next step. And you can't machine warped rotors, they need to be replaced.

 

Think I could take my car back into the shop and tell them that they should of changed my rotors instead of just machining them?

And this jerking problem when I come to a stop is getting worse. Seems like the jerking happens between 2nd and 1st gear. Tranny, brakes, any ideas?

 

I am having the same issues that you are. I replaced both of my axles and it still shakes under acceleration. I think one of the axles was defective though, so I will check it out. I would get the rotors replaced because warped rotors cannot be machined. I would swap the axles out though, just to be safe.