Miss at idle, Stuttering from 40-60 mph, no CEL. I'm at my wit's end.

Rivers

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I'll give a little background on the car... '01 with about 140,000 miles on it. Last September it snapped a tensioner, and sat for several months before we tore everything apart. We replaced the timing chains, guides, and tensioners. After all that, it ended up not starting. So we replaced the fuel pump, fuel filter, and threw in new spark plugs as well.

It runs incredibly smooth now. Smoother than ever, but every so often, when I come to a stop, it'll have a slight miss or shake to it. Less often, when going from 40ish-60ish it has a stutter to it that is more noticeable, and it also is experiencing a loss of power in general. It just doesn't accelerate like it used to. We tried fuel injector cleaner, and that helped clear up the miss it had when we first got it running again. Cleaned the mass air flow sensor, and that didn't help at all. We noticed that there was a little sputtering coming out the drivers side exhaust when it would hesitate, so we moved all the coils from the drivers side to the passengers, and vice-versa, and the drivers side exhaust still displays the puttering, so it's not the coils. That led us to believe it was the fuel injectors, tested 'em with the ohm reader and they tested fine, but maybe they're clogged from dirt getting in the line when it was disconnected? Anyway, it's not throwing a CEL light for this, and I'm really puzzled as to what this could be. One or two people said maybe we did the timing chain wrong, but I don't think that's the case because I would expect it to be more consistent like it was when the tensioner snapped and the chain skipped a tooth, and besides the slight shake that only happens every so often, the car runs quiet and better than ever. Any help or advice on what to look for would be gladly appreciated.
 
1. You've done nothing to eliminate marginal coils as a suspect. Generally speaking, coils do not last 140K miles on the LS. You really should change all the coils and plugs. Verify that the new plugs are gap'd to 1mm.

2. Did you inspect the valves? Did you do a compression test? A leak down test? There's a good chance that you bent one or more valves, and this would also cause your symptoms.
 
I'm going to go check the plugs right now, because I'm almost certain that they aren't gapped to 1mm. I've replaced two or three of the coils over the years of me owning the car, but never all of them at the same time as you guys on here recommend... but man I hope it's a coil now. A bent valve means all that work for nothing. I'll try the compression test later today. Thank you.
 
I think I would suspect the coils over bent valves. I can't see a car with bent valves ever running smooth, as he reports the car sometimes does. However, marginal coils can work correctly at times and incorrectly at others. A mechanical defect cannot get better, but a failing electrical part can.
 

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