Have your mechanic put the scaner on the car and look at the fuel numbers. You know the Block Learn #' and the Integrator #'s and the O2 sensor cross counts. Those will let you "see" what the state of the fuel trim is. The 90's have the injectors that will eventually fail, via shorting coils, due to the modern alcohol fuel additives. The ethanol in gas now was not an additive when the injectors were designed, therefore the coil insulation is not resistant to it.
You are sure the coils, plugs & plug wires are okay? There is no SES light indicating any stored DTC's? You're sure the fuel filter is not blocked? Those are some of the simple things to "eye ball".
The behavior you describe sure sounds like the primary injectors are shorting out. When they short out they do not shoot any fuel and you wind up with a big miss or skip. That miss causes the D/M fly wheel to "Knock" because of the uneven power pulses from the cylinders. If you stand behind the car does it smell "Lean"? That's another give away on a fuel issue. If you pull the plugs you might see which are not getting any gas...they look to clean.
The symptoms you describe are almost exactly like what happens when the injectors start to short. Usually there is a slight miss that gets worse as the motor come up to normal operating temp on the coolant. The coolant temp is not affecting the injectors. As the injector coils are worked more they get hotter and if they have shorts the short becomes more noticable, you get a bigger miss. OH, forgot this: you may want to verify that you have the correct fuel pressure also. You do have a FSM from Helm for your model yr?
Tom