The ignition timing should be set only when the engine is fully warmed up and is idling to spec. Did the pointer (aimed like the sight on a gun) on the timing belt cover align perfectly with the red mark?

Is the CEL on now?

Was the distributor turned fully in one direction to set the timing? If you can't perfectly set the ignition timing, then check the mechanical timing of the cam and crank:

 

No CEL, and I only had to turn the distributor a little bit. The red mark was about an inch off of target. I think its perfectly centered.

 

NOTE: When I swapped out the ignition rotor , it was stuck real good on the shaft and I had to use a hammer. No visible damage tho

 

So the red mark and pointer now align perfectly and this was done with the engine idling to spec (~600 rpm for MT) and the service connector jumped?

Did you reset the ECU after setting the timing?

If you think the rotor may have been damaged, then replace it.

Do you have the plug wires in the correct firing order on the distributor? The cylinders are ordered 4-3-2-1 from the distributor to the timing belt.

 

I did replace the rotor but I had to use a hammer to get old one off. Engine was probably idling around 800 and it was warm. plugs are in correct order according to your diagram. I really dont know what else it could be. Also what is a cylinder sensor cause that was one of the codes before i cleared them out.

 

You possibly damaged the distributor getting the rotor off. Pull the plugs and the distributor cap to inspect them. You should also remove the coil and igniter unit from the distributor and have them tested at an auto parts store. You could test the coil yourself if you have a multimeter. Is the inner cover missing inside your distributor?

 

Code 9 has not returned, right? You can still test it by measuring resistance of this distributor sensor:

 

I replaced the coil because after I got the rotor off the coil didn't work anymore, it had hot spot on the housing. The cap is brand new and has the inner cover. If the ingniter is bad, wouldn't I not have any spark at all? I have NGK plugs now but they are the ones that came with the car, I have new BOSCH Platinums, I guess I can put those in and give it a try...

 

Ok I replaced plugs and it seems to accel better now. Now when I hold the pedal down it bogs down until about 3100rpms and then rev up like it is suppose to, where as it used to just stay bogged down and then backfire.

 

Making some progress. When coil goes, it will often take the igniter unit with it. The igniter can be intermittently faulty before it completely fails. Have it tested.