Sat for 9 months, Won't Start

So here's my dilemma. I'm in the military and have deployed for 9 months. I do what I always do when I leave, disconnect the battery, put it up on jack stands keeping the suspension loaded. Well and hook everything back up crank the motor to get the oil flowing with the fuel cut-off (pop the IFS switch). Took battery to Autozone had it charged all the way up. Reset IFS switch. Cranks like a champ but won't start. Since i just got back have money to throw at it. i can see that it wasn't getting fuel pressure, and it threw 1233 FPDM offline. Changed that. Then was getting low fuel pressure. changed pump. Got back to 40 psi. Still nothing. If I floor it it will stay running but only at 500 rpm. as soon as i let off of the gas pedal done. I did change TPS cam and crank sensor no luck. Did some trouble shooting thank to posts from WM Burns. suspect MAF. a few days later I go out to the garage, and start it up. Scared the kids! it's alive. Or so I thought. Next day I go back out and same thing. idles at 500 rpm if I have it floored. The PATS light has always flashed with the key out and proves out when going to start. But to be sure and to optimize the mods I have done to the vehicle, I had JMS make me a tune to disable PATS since it was $75 bucks. well I'm still seeing the theft light so I'm calling them when they open on Monday. There is one thing that I noticed is that the check engine light stays on. it does not go out with the theft light. I left it one time for 5 minutes key on engine off, still on. It does go off though when i keep it the engine idling. I'm at a loss. I did do checks according to post put by WM Burns and since i do have some money to throw at it changed out the CCRM. I was able to get another PCM out of a running 4.6 5 speed for cheap since it was totaled and put it in to see it PATS would do what it is supposed to do and flash when trying to crank and it did so I know that the PATS in the car is working properly. Other than the tune that was added, this setup has brought me loads of fun since 2009 so its definitely not a modification issue. Any help is greatly appreciated. I have drained the tank and added fresh gas fuel filter etc. This is my last weekend to mess with it for awhile (up coming training).
 
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No everything is fine. car is garage kept and up on jack stands. I've been through the wiring just to see if there was a possible break anywhere. took off the passenger front tire to check wiring from the CCRM. Everything is good. i just put in autometer gauges while i was waiting for the tune to be made and had the dash apart. everything is good. did fuse checks like WM Burns posted in other posts. Everything in under the hood and in the car is good. power is everywhere it is supposed to be when it needs to be. I get pops when just cranking. If I step on the gas pedal i can keep it idle at 500 rpm. And that's at full throttle. After I changed the MAF, it started right up. next day it went back to doing the same thing.
 
Not a PATS problem! Why? Because it STARTS! Once started, PATS is out of the picture. PATS isn't going to make the car run poorly after the motor has started.

Recommend stop throwing parts at it.

Is the fuel rail pressure sensor intake vacuum line connected and leak free?

Are there any intake vacuum leaks? Tell us about ANY DTC codes.

What is the fuel pressure as measured by an external gauge and reported by the PCM?

Do you have an ODB2 scanner? This could make very short work of this problem.

Would be real handy to know what the PCM "thinks" the MAF flow, IAT, and fuel pressure is.

What is the voltage across the TPS with the motor on?
 
The car only started once. So i'm chalking that up as a fluke. My live wire picked up 1233 FPDM offline. I changed the the sensors because they are original. the motor has 3,000 the sensors 128,000. It will have a random pop unless it gets floored then will only idle @ 500 rpm. let the gas go it dies. fuel is definitely there. i only did this three times and then shut the fuel off to get all the gas out of the cylinders. need to get a scanner. the livewire will only read the parameters when i keep the engine @ 500 rpm and it is spitting out the exhaust. I will be putting down the wrenches for a while. Duty calls see ya in a few weeks. thanks for all the responses. wont see my car till May.
 
sethahoward it my honor to serve this great country. I've done it for 15 years and I'd do for another 15. Now that I'm back I was able to get the car started. I went and reseated the coils. Went to drive and the the car threw 0300 (multiple misfire). Continued to see what cylinders would show up. 0305, 0307, 0308. Just the luck. switched back to the old coils and everything is fine. The bad part is the new coils are weapon X level 2 450.00 and since i ordered these while i was deployed I was unable to send out the warranty card to cover them in time. And Brothers Performance (where I ordered them from) says that Weapon X Performance no longer sells them individually (they called to let me know after I ordered replacements). I had been running weapon X coils since '08. I just put three of the old ones in and it's back! nothing like setting off car alarms with a crack of the the throttle!!! Thanks for all the replies. Consider this problem solved.
 
Good to hear. I had some frutraions with my car recently. It was doing exactly the same as yours but mine turned out to be a bad wire to the FRPS and a charging issue.

Chalk another thanks also...

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