Just my own notes here.. I'll update as I make progress. I'm writing this down anyway, so might as well do it here just in case it helps someone else. MODS: If this doesn't belong here, please give me the opportunity to copy it out before you delete it 
This may (very likely) contain errors. If you see me doing a dumb, call me out PLEASE. Follow my notes at your own risk. I have not yet completed this quest.
The Challenge: I am trying to run a manual swapped vehicle with in OS intended for an Automatic. In my case I can have an engine that performs like it should, or a speedo - but not both.
In at least this particular vintage of trucks, the speed information is transmitted from the TCM over the "High Speed GMLAN" CAN bus; the data is received by the PCM and BCM via that CAN network. The BCM converts the engine data to the GMLS (Low speed data) bus which feeds the cluster; the cluster does not have CAN nor a direct speedo input. Unfortunately, the instrument cluster doesn't get speed information if [ECM] 439 is set to MANUAL in the tune. VCM scanner still sees the speed, regardless of this setting, but evidently the E38 doesn't send it out to the cluster in the case it's set to manual. This OS wasn't intended to do this, so it doesn't. Side thought: There may be something in the EEPROM of the instrument cluster that affects it as well - and could cause this whole experiment to fail. Time will tell.
This would also apply to folks who have put an LS in some other vehicle that already had a manual (hypothetically let's say it was a 2005 GMC Canyon) and were of suspect enough intelligence to also swap in the instrument cluster and BCM. I assure you that if someone were to try that they'd have many other challenges to overcome too, and they really better like wiring and especially splicing wires. Don't ask me how I know, I am aware of the 5th amendment. What I can tell you is that a 2-oh-5 GMT355 has neither a High Speed GMLAN nor GMLS network (only Class II Serial) so its instrument cluster has no hope of talking to a GEN4 LS, at least not without the support of its original P12 PCM somehow (overlay harness).
Proposed Solution: Upgrade to an OS that was intended for a manual trans.
Current OS: 12614088, VIN 3GNEC12037G134210, 2007 Chev 1500
2006 / 2007 E38 OS compatibility:
12602922, 12605732, 12605898, 12607218, 12608677, 12609099, 12611833, 12612281, 12612291, 12612381, 12612739, 12613889, 12614088, 12614676, 12614682, 12616478, 12617569, 12628981, 12628988
Other model years with the E38 PCM exist, but it's likely that the hardware changes with time, so stick with the same model years.
TASK: Find a vehicle with the feature set you want in the repository, and confirm it has an OS within that list.
07 Vette 6.0 Manual: 12613889 (From repository)
OS Upgrade:
The full OS swap can't be done in HPt; you have to use GM's SPS application through the AC Delco Tools site.
Accessing SPS requires registering with AC Delco Tools, which is free.
SPS access is paid based on the # of vehicles you want to do. Once you buy a subscription, it's good for 2 years. If this takes longer than 2 years I may be in trouble. From the subscription page:
There are two limitations on the per-vehicle programming. The subscription expires based on whichever of the following occurs first:
1. 24 Months.
2. The number of programming equals the number of programmable modules in the vehicle.
Question: Does that mean you can program the OS only 1 time?
J2534 interface is required - seems to be many available - pick based on your preferred price point and trust level.
Warning on AC Delco site:
WARNING- USE OF COUNTERFEIT "CLONE" GM MDI DEVICES will result in your account being locked. Aftermarket J2534 devices are not impacted.
So don't do that. I'm betting that J2534 isn't impacted because it isn't a GM specific protocol.
What is J2534?
J2534 is an interface standard designed by SAE and mandated by the US EPA for vehicle ECU reprogramming. Its purpose is to create an API
which would be adopted by all vehicle manufacturers,
allowing the Independent Aftermarket (IAM) the ability to reprogram ECU?s without the need for a special dealer-only tool.
How thoughtful of them.
When you get into SPS, it appears you will select your OS based on the VEHICLE VIN, so grabbing that from the calibration downloaded from the repository is critical.
VIN: 1G1YY26U975113744
I think SPS will give you the most recent OS for the VIN you feed it, which I expect won't match the OS you found in the repository. That's fine, so long as you didn't mess up the VIN and you end up with an OS for a Lada Niva. Double / triple check.
Important When you reprogram an ECU with SPS, it's going to update the VIN and OS (maybe the serial number?) to the new one; this means you will lose your HPt license for that hardware, requiring you to buy more credits to continue tuning that PCM.
Feedback from HPt Support:
Licenses consist of three pieces of information. They tie in VIN, Serial Number and OS. If you change any of this information you will break the license and have to license the new combination of information you created. You will need to hold a license for the file you are writing as well as the vehicle you are writing to.
I think the the best approach is to locate another E38 to license after the OS swap - then I'll still have a spare, licensed E38 for an Auto application. I suspect it may be possible to program the original PCM back to the Silverado VIN, but unless the VIN, Serial and OS match, HPt will want a fresh pair of credits for it. You might not care about having to relicense, or you may have unlimited access to that platform; but I'm cheaper than a $3 haircut.
More to come...