Engine miss, or is it?

I picked up a '96 Sierra 4wd, 5-speed with the Vortec 350 about a year ago. I've noticed a "miss" after the first couple months so it got a tune up (Bosch plugs, wires and standard cap & rotor and fuel filter). The miss persists. Picked up Chilton's and Hayes manuals and started in on the sensors (all checked out OK). Took it to the local dealership, but after 4 hours and three test drives (one by the shop foreman) they said it is running as designed. After disagreeing, they admitted they couldn't find a problem because there are no hard or soft codes.
I pulled the upper (composite) manifold and found oil on the lower manifold, carbon on the inside of the upper and throttle plate. Also found a pinched O-ring, but new O-rings and PCV didn't fix the miss either.
The pervious owner had the injectors cleaned and fuel pump replaced for this SFI. Think he was chasing the same problem.
The miss is most noticable in 3rd gear, 1/3 to full throttle, between 2 and 3k rpm, but I notice it in 4th and 5th as well. At an idle it even sounds like its missing a cylinder or two. Some days are worse than others, but climate, fuel grade and load have no effect.

Any help/leads would be spectacular.  

At this stage you need to do a compression check to check the health of the engines internal parts (rings and valves)  

I've been threatening to do that...I want to pull the valve covers, too, for S's and G's.
I know the bottom end is sub-par; it started knockin on start-up last winter and I noticed and intermittant noise at an idle. Thought the T-chain was slapping the cover, but found that the cover is plastic and the chain is fairly. Also the rod and main bearings have seen some dirt. Should have replaced the crank (scratched, too), but only had time (and $) to roll in new bearings. Thought the knock sensor was picking up the slop and retarding the timing cause every once in a while it will "clean out" and run like I expected the Vortec to run. Most of the time performance is pretty flat.
I've been concentrating on fuel delivery due to the intermittant nauture and it's 150K miles, but...
Thanks for the quick response. I'll dig out the C-tester this weekend.  

For what it is worth, 350 Vortec's also run better on 89 octane or higher fuel. Post what you find from compression check.  

verifiy sparkplug gap and look closely at sparkplug color when doing compression test!  

I prefer to run the mid-grade. Premium if I'm towing, but in my area, we're forced to use 10% Ethanol. Would blame the alcohol, but had this problem before the E10 law. Didn't get to the C-test. My Snap-on dealer loaned me his Modis and spent the weekend messing with it. Found that the distributer was off 7 degrees (should be 0 +/- 2 and was at -7). That made a difference in performance, but the "miss" is still there. Also looks like one of the post-cat  O2 sensors is weak/lazy. Reads half of the other once everything else is up to temp and stable, and both post-cat O2 sensors change nearly as fast as the pre-cat O2's. If the c-test results are good (static and running tests), think I'll change the O2's and pull the Bosch single platiums for Delco double plats. Didn't find a readout for fuel pressure. This is still a ?. The previous owner had the fuel pump replaced and my local dealership said the pressure was good, but by 4k rpm it falls on its nose. The Modis also recommended verifying the distributer gear is not off a tooth. I'll post when I have results. Thanks for the help!!!  

A pump can have good pressure static and drop when demand increases. You might replace fuel filter on frame rail.  I do think lack of high RPM power and miss are not directly related though. Still need to do a CR check to see if you have a burnt valve. Also on secondary O2 sensors, do not worry about them they have no control over engine mixture. They are there for emission self test feedback and engine light for this and nothing more. Pre CAT O2 sensors control mixture and BWT, the reading on them will be far from steady too so do not make much out of that. The only time they will be fairly steady is when engine is under a sustained heavy load.  

Plugs, wires, cap, rotor and fuel filter were the first things I changed. I put another F filter in this spring and cut the old one open, but it was fairly clean. Good info on the O2's. I've been told they should be changed whenever plugs are changed. Dosen't sound like that is true.
Plugged in Modis for drive to work...knock counts increase rapidly (sometimes 200+ in just a couple of seconds)in the rpm range  where the "miss" occures and is bumping the timing back, but only 5 or 6 degrees. Dosen't sound too bad, but makes me wonder how much of the detected knock is the loose lower end. Its starting to knock on start-up again, now that the mornings are colder. Engine feels stronger now that cam retard is back to "0", though.
Lots going on this week, but will try to finish C-test before the weekend (my boy wants to go hunting again). Thanks again.  

This is interesting in that you have some good data. The way the knock sensor works on a Vortec is that it takes a snapshot of background noise at idle and establishes a base line noise level to use for detecting knocks. Then ECM takes this data and uses it to modify timing curve so that engine operates smoother though with less power. It does this by remembering the operating parameters when knock occurs and keeps spark retarded so that it is not being jerked around and causing engine to feel like it is missing under heavy load. Your data tends to suggest that you are no feeding it enough octane fore your conditions and load. Honestly though many strive to use cheapest possible gas, a Vortec does better on 89 or better octane all the time as 9.1 to 1 CR is a bit much for 87 without timing trickery. As a engine gets older octane requirements tend to increase because a little carbon builds up normally in chambers raising CR and if a little oil is being used this also lowers octane of fuel mixture. Run tank down and then put some 89 or better in it and then pull ECM fuse for about 10 minutes to clear its memory and put it back in learn mode and drive it and see what data says. Also if bottom end is a little loose it could in theory possible send false knock signals to ECM. Also if you are using 5w30 stop using it. The merits of it is somewhat debatable in a new engine and it merits in a older engine with wear are even more debatable. Use 10w30.  

Shortly after I noticed the knock I started adding Lucas oil additive, but swithced to 10w-30 after rolling in new rod and main bearings, last winter. Can you believe they're putting 0w-30 on the shelves?
I also ran nothing by 91 for almost two months straight, this past spring. We noticed a boost in power, but the miss was still there. Don't remember pulling the ecm fuse, though. I'll try that and fill the tank with "clear" premium (no ethenol) the first time.
I like this Snap-on Modis, but sure it's out of my price range and I'll have to give it back pretty soon. What would you recommend? Been looking at the interface module from Jet that I can connect between the ALDL and my laptop.  

Definetily need to see compresion test. Bottom end might be loose with a little piston slap. Curious to know if cam is good? You will figure this out on compression test. Had a engine with excessive valvetrain noise and caused the engine to retard once. Rerun the valvetrain and knock went away. Engine was set up very cold and as it warmed up everything loosened up on clearance and knock sensor pick up on the noise. Rare situation but it happened.  

You know what you could try here is get a new knock sensor b do not install it in block and secure it in engine bay in a padded wrap with the signal wire and a ground hooked up to it so ECM see a good sensor but sensor see no data from engine. If miss is still present then it pretty much rules out knock sensor spark retard. Also have you replaced Crank Position Sensor on front of engine by damper? There is also Cam Position Sensor but that is simply a new name for magnetic pickup in distributor. While it does not control/fire spark it is part of a feed back loop for error checking.

Also I have had a Injectronic.com CJ3 scanner for a few years and have been quite pleased with it. It has real time data support and graphing on unit and a feed through for a laptop too. It has been superseded by CJ4 now which is even nicer.  

It's a roller cam...they don't wear out, do they? wouldn't think so unless a lifter roller seized or ??? Looked it over when I had the oil pan off and didn't see any unusual wear or galling.
Couldn't I remove the existing knock sensor?  I assumed it was threaded into a blind hole. Also, how does the knock Module factor in, if at all?
One of my troubleshooting steps was to disconnect the various sensors (one by one, at first)until the miss when away. As soon as I pulled the plug on the crank sensor the engine died and wouldn't start until the sensor was reconnected. Nothing happened when the cam sensor was disconnected, but it checks out with a multimeter. If the crank (and/or cam) sensor is a possible suspect I'll replace it. I have not replaced any sensors yet because I wasn't sure where to start / didn't have enough info.
I'll try the remote knock sensor test tomorrow and pull the ecm fuse to be sure we're starting from scratch. I'll look into the scanner, too.  Thanks!!  

All the checks you've made but still no compression test what's up. It just takes a little time and you'll learn a lot about your engine's health and whether you should spend more time on this engine or get a new one on the way!! Its a easy check just time consuming.  

Yes, but time is the one thing in short supply for me.
Here's what I found out;
Hi cylinder was 195 psi, low cylinders were 180 psi.
1-195, 2-185, 3-180, 4-190, 5-185, 6-180, 7-190, 8-190.
Plugs looked ok. Light brownish on the electrode, crispy black build-up at end of threads. It uses less than 1/2 a quart in 3K miles. Pretty good overall, I think.
Had to order the knock sensor (yes, there is water behind it!), but plan to try the "clear premiun" and learn-mode this week when it gets low on crap-gas.
Is pulling ecm fuses dirrerent than removing ground from battery? I know that on the busses I work on stuff like that makes a difference.