This is the procedure i followed to index distributor.
Connect a voltmeter to the distributor sensor connector by removing the end seal and carefully back probing the connector. Connect the positive lead to the sensor output pin (pin 3, either a tan wire with a yellow tracer or a gray wire, depending on vehicle application). Connect the negative lead to the sensor ground pin (pin 2, a black wire with a light blue tracer). Rotate the engine clockwise as viewed from the front, until the number one piston is at Top Dead Center (TDC) of the compression stroke. The timing mark on the vibration damper should line up with the zero degree (TDC) mark on the timing chain case cover. Continue to rotate the engine slowly clockwise until the V6 or V8 mark (depending on engine type) lines up with the zero degree (TDC) mark on the timing chain case cover. The V8 mark is 17.5°after TDC and the V6 mark is 147°after TDC. NOTE: DO NOT ROTATE THE ENGINE COUNTER CLOCKWISE. IF THE ENGINE IS ROTATED BEYOND THE MARK, RETURN TO STEP 2 AND REPEAT THE PROCEDURE. Loosen the distributor clamp bolt. With the ignition switch in the ON position, rotate the distributor slightly in either direction until the voltmeter switches between the sensor transition point of 0 and 5 volts. Adjust the distributor as close as possible to either side of this transition point and tighten the distributor clamp bolt to 19-26 N-m (170-230 in.lbs.) .

 

The reason i beleive it is lean is i used a volt meter on the O2 sensor and drove it. At the point that the issue comes, it drops to .18 volts. Also when i changed O2 sensor it is white. I have not pulled plugs but thinking i should to verify a lean condition.

 

I can see what they're asking you to do, but for all this to work, you still need to get the distributor into it's physically correct position, and once you have that, this electrical setup should do the setup for the cam sensor that's in the distributor. To do this physical setup, you still need to get the engine to TDC compression stroke on #1 cylinder before you slide the distributor into it's hole. When you seat the distributor, the rotor should pointing at where the #1 post on the cap would be. I've found on other Jeep engines that the TDC mark on the harmonic balancer isn't always where it should be, so I usually probe for the TDC by using something "soft" like a stick or pencil to catch the high point of the piston movement and then check this against the balancer mark for future reference - all this must be done by rotating the engine in one direction only, turning the engine backwards, the "slop" in the gears and chain will give you a bad reading. If you do need to turn the engine the other way for some reason (like getting your stick out of the spark plug hole), go most of the way around the right way to get the chain and gear tensions back where they are in normal engine running.

As I've mentioned, I think that your engine is too far advanced and I'd be looking at the physical distributor setup or the timing chain positioning to make sure you have a good base for fine adjustment. There was another jeep owner on this site that recently had difficulty with timing a 5.2 - the timing chain markings/installation appear to have been the issue. You may need to take the valve cover off to make sure everything is synchronized mechanically - the cost of doing this is incidental (a gasket or bead of RTV). At 10 degrees BTDC, the engine will idle fine, but maybe not the best, but when you increase RPM, the ECU will start to increase the advance, and at 30 degrees BTDC, you're starting to "push up hill" - the detonation is pushing against the piston for quite a few degrees of rotation before it can give you whatever power is left on the down stroke. Thirty degrees is a BIG angle.

 

Here's a link to the other thread on 5.2 timing issues. If you do some research on the internet regarding 5.2 distributor installation, you'll see reference to the physical approach I mentioned. Without this mechanical sync, the ECU can't make complete sense out of the crank and cam positioning info it's getting from those respective sensors & you can get some odd-ball timing issues. Essentially, everything works the same as it did on the old engines except that the ECU replaces the old mechanical advance methods with calculations and solid state switching.

 

Timing is good. Had the intake off fixing the plenum leak checked valve timing then, and indexed the distributor again.

I did figure out that i had the neutral safety switch wired incorrectly. Clipped the wire to the pcm for that and now it runs worse. Pretty flat in all throttle positions. It also threw a check engine light the other day and had map sensor code(13) and tps code(15) reset them drove it a bit and got the tps code back. Tested both tps and map sensors, both test good, again. Reset pcm today when i did the intake and i am getting no codes again but still running poorly.

 

Well dusted, I've run out of ideas, did you check the advance angles again after resetting your distributor? What did you do to re-index the distributor? With the intake off, you still can't see if #1 piston is at TDS and that everything else is all lined up to the true timing requirements.

If your TPS is malfunctioning, it could give you some weird results and sometimes the OBD1 ECU doesn't pick up on that. I found that the tests given in the service manual don't really tell you much unless the unit is really broken. In the past, I've tried replacing the TPS with one that I knew worked to see if I was on the right track & occasionally I got lucky and found that was the problem. If a known good TPS doesn't give you different results, then your problem is elsewhere.

The neutral safety switch is only there on the automatic, the manual had nothing and the connector was jumpered to make the ECU think the safety switch was always "safe" (The ECU was the same for the auto and manual configurations). If the ECU didn't get the "safe" signal, it wouldn't let you start the engine, so if you cut something to the ECU, it couldn't have been that line. On a manual transmission, the switch is activated by the Reverse gear selection and is for your backup lights and not to give the ECU the safe signal. You might want to get a service manual wiring section for that engine & ECU and make sure the wiring & connections are all good.

 

I have read that having the nss grounded can cause power loss issues because of the computer thinking its in park. Could be an issue for obd2 only. Just something i tried while troubleshooting. I jumped the start wire to get it to start.

Engine was at tdc, checked that and checked valve orientation with intake off. All was correct. Set distributor by method i posted earlier as it was already in correct position just needed cam sensor set.

I have tried 3 unknown tps and all show same symptoms.

Thanks for your help. I am by no means a beginner with this stuff and this thing just has me stumped.

 

I'm doing a bunch of reno at home, so I have a lot of time to think about other things - here are the fruits of my labor from this last thought process.

Even though the engine is somewhat computerized, it still needs the same things as gasoline engines have needed all along - fuel & spark. Since you feel that the timing is right on, then the engine must get both fuel and spark at the right time unless something's broken(the computer's involvement in the timing equation means that it calculates when to inject fuel & provide spark and then initiates both). Since the engine starts and, to some degree, responds to your demands, tells me that the fuel & spark are both getting through, and with the correct physical setup on the timing, it should run fairly well and not bog down when you accelerate. So, the way I figure it, if the timing is good, then the combustion must be rotten and a couple of things might cause this - bad fuel/air mixture, or bad compression. If your injectors are firing at the right time, but not spraying enough fuel, you could get the lean condition that you were talking about - this would cause high heat & wouldn't be good for your valves. If the valves were already "lightly toasted", you'd get a poor combustion - this would also cause the engine to bog down & essentially rpm limit itself at some pretty low rpm like you're currently getting. Burned valves often cause a backfire of the unburned gasses since the burn inside the cylinder was poor, but you don't always get that.

I know you checked the fuel pressure, but you can't tell what the injectors are doing from that, so I'd focus on some positive stuff to get some more information. I would have a look at all the plugs to see their color & gap - this would at least give me something to do while I was scratching my head for other brain waves.

 

So today i tore into the wiring harness. Checked everything and did some tidy up work. Checked continuity of all wires. Added a couple more body to engine and battery to body grounds.
I am now 100% certain of the wiring.

My feeling on this is that i have a bad pcm. It is a junkyard unit, no knowledge of its past. I have changed every sensor with at least one other and there has been no change. On top iof that i electrically tested them. Chances are the sensors are good.

I am going to pull plugs and check color and compression tonight. When i changed plugs a couple days after i got this up and running they all were a nice tan color, no issues. Put new plugs wires, cap and rotor on at that time.

It doesnt run, start or idle like its got compression or valve issues, but test will tell all.

I have been getting a bit of backfiring when its cold. Warm it never does. It hasnt been running consistently. It is always down on power, but some times it runs worse than others, some times the idle is high(1000rpm) and the idle surges up and down a hundred rpm or so. If i shut it off and immediately restart it idles normal.

 

A good used engine control unit for that year shouldn't set you back too much and you don't have the security system problems of matching the ecu to the rest of the system like you have in newer vehicles.

I've found that a compression test on it's own won't always tell you how good each cylinder is. The air compression that takes place at TDC is a lot less than combustion pressures and valves or rings that have very small leaks won't be picked up on a compression test but are noticeable during running. A few years ago I had a 4.0 liter jeep engine that was fairly new, but the distributor had been installed improperly giving the engine a retarded spark condition - the engine was able to start and the flames through the exhaust valves caused a very slight burn. This burn was enough to give me some of the symptoms that you have in terms of lack of power and rpm limiting, but the intake valves were also affected enough to allow some of the hot gasses into the intake giving me TB backfire under load. I did a compression test on this several times and got no indication of the fault, but when I hooked up a leak-down test rig, I noticed that most of the cylinders had some degree of leakage.