I'm hoping for some kind of sanity check here...

This is a classic truck with an L92 6.2 E38 and T42 4L80e. The truck starts and runs great, the issue is with 3rd gear and 4th.

This is a complicated issue, I will try to put most of it down along with a log soon.

Basically everything you physically feel and see on the tach/speedo is that it has 1-2-3 gear just fine, no overdrive. Can't get it to command 4th, won't go into 4th under any circumstances.

however, if watching a scanner (both EFILIVE, and a very nice Snap-on) it digitally shows it going 1-2-4. The ecm commands 4th, the iss is 75% that of the VSS, and no check engine lights. The computers think they are in 4th gear. But they are not.

While in this state we are driving down the road at 60mph, all the electronics say we are in 4th, but the truck physically is in 3rd the best we can tell (it feels like 3rd and the speedo, tach, rear end ratio agree we are in 3rd)

*sometimes* under light deceleration I can pull the shifter down into D and the ISS and VSS line up at basically 1:1, but its not perceivable physically while driving. If we get back on the gas they immediately show 4th gear ratios, or if we put on the brakes the truck will go into 2nd and the iss/vss reflect this.

Also, when pulling the truck down into 1 with the shifter, all is good. Pull it up to 2nd, all is good and it goes into 2nd. Pull it up to 3 and NOTHING changes as far as physical gear change, rpm, ISS/VSS, nothing EXCEPT the scanners show 3rd gear. You can stay in that state forever (actual second gear but ecm reads 3rd). You can then pull shifter up into 4th and you feel the shift to what I would call 3rd gear, but again, the ecm and vss are now showing 4th gear numbers! Im about to pull my hair out!

The very basic issue I'm seeing is the ISS/VSS showing 4th, (75% overdrive) but the truck in every other sense being in 3rd. How is that possible? I've always seen the ISS and VSS to be a very cut and dry rotation count. is there some way for this to be skewed???

some more details...

-We have quadruple checked the harness against stock gen4 4L80e GM diagrams.
-The truck is on its 3rd transmission (1st was used with issues, then rebuilt it, then went and got a completely different rebuilt trans from a different reputable shop. Both of the final 2 were doing this exact issue).
-We've tried an 07 operating system in both an e38 and t42 match. We've tried a 2008 van 6.0 matched e38 & t42, we've even tried mixing and matching the combos of these 2 e38s and t42, we always end up with this same result.
-We've checked grounds until we are blue in the face.
-the truck has never been right since its completion a couple months ago, the problem has been there the whole time, it wasn't something that developed after the fact.
-there are no CELs at all
-the ONLY thing that is left is to start pulling the harness back from its installed location. There are a couple places where the owner got crazy with zip ties and there are some data wires awfully close to some power wires. In my experience they aren't close enough to be an issue, but that's about all we have left at this point. Seems like if there was some sort of data interference we would be having more trouble than this. Other wise the truck is flawless. If I told you it had a th400 in it and to take it around the block you would come back saying it ran awesome.

I don't expect anyone to diagnose this over the internet, especially without a data log (yet) I'm really hoping there is someone that has seen this crazy issue before and can help out of experience. If nothing else it feels good to type this out and get it off my chest. It makes no sense. Thanks to anybody who might be able to give advice.