I have a 2003 LS swapped 5.3 and an 2002 4L60e transmission in a1962 C10, drive by wire throttle . It’s a rebuilt transmission but unsure of the mileage. The issue I am having is that in overdrive, it shifts fine from 1st. To second, but when going to 3rd it basically like going into neutral. I can then sometimes come to a complete stop and shift through the gears manually and it will be just fine, sometimes not. Transmission is full of fluid and it does not smell burnt. I also recently had an issue with the transmission going into limp mode. Loosing power and only having 2nd and 3rd, I checked resistance in the harness from the CPU to transmission plug and ended up replacing the plug which fixed the problem. Been driving it for several hundred miles until this problem occurred. I would think if the bands/clutches were fried it would not be intermittent. Could it be the shift solenoids?

 

Unhook the harness and see if you can do a manual 2-3 shift, If so and its solid then hook back up. clear codes and if possible datalog shifts , also any codes stored?

 

I'd venture to say the rebuild is a flop

 

My hunch is that there are significant leaks in the 3/4 clutch circuit; this is basically a given with cheapo rebuilds.
When the line pressure is high enough 3rd gear will engage, otherwise not. Perhaps when you are shifting manually you are giving more throttle which raises the line pressure.
Frank's test may succeed because disconnecting the harness forces max line pressure, but then not tell you much. If it fails, we know the trans is toast.
Most likely it will need a careful and complete rebuild from someone like Frank.