[ImperialCrown]

Welcome to Allpar.
The injectors are supplied (+) from the ASD relay on the Gn/Or wire from a splice (S100) and are grounded sequentially/individually on the (-) side per the firing order by the PCM through connector C103.
Splices and connectors are the weak links while harness rub-throughs and wire breaks/pinches can also happen.
The injector 'sync' timing signal is determined from the cam sensor. I doubt that the cam or crank sensor would pick on the #3 cylinder in particular, but would be more of a general type cylinder or injector fault code.
You want to check the Yl/Wt wire from the #3 injector terminal to the PCM terminal. If you have no test light blinking at the PCM terminal and the PCM connector terminal-to-PCM pin continuity is good, then the problem may be in the PCM itself.
A factory service manual and powertrain diagnostic procedure manuals may be useful to you here. I don't know what modifications may have been done for the supercharger installation.

 

[dana44]

I have to agree with Imperial Crown as far as the cam/crank sensor goes. I had a belt strip the cogs and in turn replaced the cam sensor and crank sensor, both non-factory but good NAPA units. I spent a year dealing with intermittent misfire, never a specific cylinder or injector. It turned out the cam sensor would throw a fake ground or something else through the material the cam sensor was made out of, factory sensor fixed the issue.

At the same time, based on what you have done, good compression, good injector, good fuel pressure, and the statement of good everything else, next step is, wiring first, PCM second, as IC said.

 

[nwmike]

Thanks guys, I didn't think that the cmp or ckp sensors would set that code but this is my first PT. I had probed the Yl/Wt wire at the PCM connector with a 12v test light with the engine running and saw rapid blinking, I probed one of the other injector wires there also to compare and saw the same. I had checked the continuity of the Yl/Wt wire from the PCM connector to the injector and assumed there would be power supplied to the injector OK, but because the injectors are behind the radiator and under the intake I'm not able to check for power at the injectors with the engine running. (I remove the grill and radiator to get to the injectors rather than removing the Whipple charger and intake). It's interesting that you say the power is supplied to the injectors from the Gn/Or wire going to all the injectors, I assumed it was a common ground. It sounds like I will need to open up the wiring harness and check the splices. I'll update this thread as I work to solve this.
BTW, I looked at installation instructions for the Whipple charger and the injector wires are not tapped for installation. They didn't appear to be from a visual inspection either, and it looks like it was installed by a pro.

 

[ImperialCrown]

If the Yl/Wt wiring test light at the PCM is flickering and the test light is grounded to the negative side of the battery, then power has to be going through the injector and the to/from circuitry wiring. It does sound like a complete circuit and that the PCM is switching the injector on/off to ground properly.
You might try swapping the fuel injector with an adjacent one on the fuel rail to see if the fault code follows the injector. Swapping it with #2 would result in a P0202 and #4 would be P0204 for instance, if the injector was faulty.
Did #3 go back in the #3 position after you removed them? I am not familiar with Dr. Injector's tests, but were they done with fuel pressure applied and watching a strobe of the fuel spray pattern?
The P020x self test done by the PCM looks for an inductive 'kick' from the fuel injector's internal electromagnetic solenoid after firing to make sure that it is still an electromagnetic solenoid with good coil integrity. This 'spike' can be seen on a oscilloscope waveform. A good coil will 'ring' from the collapsing magnetic field after removing power. An injector may still be plugged up with debris to prevent spraying and not necessarily set a 'P' code, you would probably get a P0303 cylinder misfire fault code as your only clue.
The danger here is cylinder #3 running lean with a supercharger boost and burning valves with preignition occurring. A cylinder compression test isn't really a good test for leaky valves/rings as the compression 'pulse' happens too fast. A better test is the cylinder leakdown test with the valves closed and listening at the throttle body (intake valve) and tailpipe (exhaust valve) for a soft hiss. A soft hiss out the oil filler hole would be from rings/cylinder wall leakage. Compressed air is applied at the spark plug hole.
You don't want to drive it like this until it is repaired if you can help it.

 

[Bob Lincoln]

Injectors have a common 12V supply, and the grounds are switched individually beween 12V and ground, to fire the injectors (or in the 2.2L/2.5L engines of the 1980s and 90s, they are fired in tandem).

 

[nwmike]

10/26/12 update, FYI this car is unlicensed and I have not been driving it. I will need to get this problem solved and get it "emission tested" before I can get it licensed. The emission test here in the Seattle area is a test of the OBD2 system with the car running, and it must be free of trouble codes to pass. I work on the car when my time allows it.
I swapped the #3 injector with one of the others and also rechecked the continuity of all the injector wires from the PCM plug to the injector plugs, all OK. I also checked for continuity between the the injector plugs, all injector plugs of the gn/or wires showed continuity to each other, the other color wires going to the injectors did not show continuity to any of the other wires. I also checked both wires at each of the injector plugs for continuity to ground to look for a short, no continuity shown. I cleared the old codes and started the car and within a minute the CEL came on and the same code P0203 was set so the problem did not follow the injector. It still feels and sounds like it's running on 3 cyl. I found a vacuum leak, plugged it and the idle slowed down, I checked the codes again and now have a "pending" P0303 (misfire) also. With the car running and the 12v test light clamped to ground I probed the Gn/Or wire at the PCM plug, the test light glowed bright and solid and the idle was not affected. I did the same to the Yl/Wt wire and the light came on bright but the car died, I tried the same thing with one of the other injector wires at the PCM plug and got the same result. The previous time I tried that the light seemed to flicker rapidly the idle slowed but it did not die (maybe the sudden dying now is due to the slower idle from the vacuum leak repair) Any suggestions at this point? If the intake gasket was bad it could cause a rough idle and a misfire condition, but would that have any affect on an injector? I already changed the plugs and wires. I'm still stumped but determined to solve this. Any ideas?

 

[dana44]

If the problem didn't follow the injector, the problem could be either the coil or the wiring itself, just isn't showing up on the probe testing, might be arching somewhere other than where you are testing. The intake gaskets are O-rings and are usually good for a long time, I have taken my intake off three times without a problem, I usually just wipe them off, check for cracks, reinstall. A vacuum gauge fluttering will indicate a leak.

 

[rmoore0949]

had a turbo PT with a similar problem last week. Ended up being PCM replacement due to bad driver

 

[nwmike]

had a turbo PT with a similar problem last week. Ended up being PCM replacement due to bad driver

Did it have an injector circuit trouble code showing? Was there still power coming from the PCM to the injectors?
One thing I failed to mention in my story is that the first thing I found when I inspected my injectors was the wires going to injector 3 pinched against a hose clamp screw head, the Yl/Wt wire had worn thru the insulation, it's possible the Gn/Or wire had also but it wasn't as obvious. Thinking that was the cause of my problem I fixed the wires, put everything back together and fired it up, but nothing had changed. When I checked the wire continuity and saw power coming from both wires at the PCM plug I ruled it out and assumed the PCM was still OK. ...but now I'm wondering.

 

[ImperialCrown]

A problem with the Gn/Or wire would likely affect all injectors and the ign coil as it feeds and is common to all these components.
If you can rule out a problem with the #3 injector and the Yl/Wt wire circuit to the PCM, then that will only leave the PCM as the last possibility.
Everything must be ruled out first. Too many times a replacement PCM doesn't fix the problem because something was overlooked.
In a way it is good that this P0203 is a constant fault. If it were an intermittent fault and hard to get to act up, it would be more difficult to diagnose as you would have to wait for it to act up in order to look for it.

 

[nwmike]

It occured to me that I never reported what solved my problem, it was in fact a bad ECM (PCM/ECU/computer). Thanks to all who replied here, it was a big help.