have you cleaned the TB ?

 

Yes, he stated that he did clean the TB.

Since the OP stated the same (or very similar) condition was happening with both the old & now the rebuilt motor, I think it has to be what they have in common.
At this point I think the 2 areas to focus on are the TB/fuel or the computer.

If the TB is clean as you said you have cleaned it, the main factors directly with the TB are a possibly faulty TPS or a possibly faulty/worn TB actuator motor.
As a "side quest" if you believe everything is checking out with the TB then you may want to give a look at the FPDM back under the spare.
These modules are "known" to break down over time & cause fuel delivery / run issues.
Especially if it looks swollen &/or cracked.
The computer "could be" the culprit, but I would expect it to have more than a low idle issue. Not that it isn't possible, but less likely.
While inspecting both the TB & computer I would also look for possibly corroded connections or chaffed wires that are providing weak signals.
You don't really have to have a rusty truck to have moisture corrode an exposed wire or connector.

 

I'm not seeing where he said he cleaned it. he stated he did a re-learn on it . you are telling him he cleaned it...

 

looks like when I was reading through, redfishtd’s description of actions got mentally lumped into the OP’s.

obviously this should be done if needed, so hopefully during his checks that have been recommended to him we will hear what he found.

 

Okay I guess you ruled out a vacuum leak but not how you did it . With a running engine spraying accelerant around the intake is not a very good test . You need to block off the vac line to the purge valve on firewall to see if that affects your engine . They are bad about leaking thru . The purge valve is normally closed you should not be able to blow through it .
Next a common failure when doing intake manifold is running the wires on rear under intake runner linkage or broken linkage . Then you need to see if this replacement manifold has the hole behind the passenger side plugged , this hole was only open for the 2004 models and the vac line was a bear to get it to stay connected . Then look at the main vac connection on drivers side rear it was recalled and a clamp added . During the 05 and later the vacuum connectors came from a metal wye on drivers side . Near where power brake connection is . The power brake booster has been known for breaking down and leaking inside .
My 05 got the defective throttle bodies that were used around 05 -06 , point is they do act up mine was very intermittent . The only answer was to change it with the latest number ,that was 200k ago . Point is they are complicated and do act up ,they wear ,the have gears/motor and circuit cards in them the tps is on the shaft so the computer can tell if its near position that it was commanded to go .
Another issue can be mixing up the lines coming off the throttle body /air filter . The passenger valve cover gets the line that is just filtered intake air not vacuum . The drivers side valve cover connects to the throttle body with a big line to suck crankcase fumes into TB to reburn them .There isn't a pcv valve its a baffle built into valve cover . It is possible to leak vacuum on valve covers ,timing cover etc .
Not knowing any dtc's you may have or readings on o2 sensors that show proper switching or your short term /long term readings and if its in closed loop
Is that seal on throttle body new . Is this a 4x4 and how are all those old vacuum lines .