Popping and stuttering after Efi install and rebuid

That is unfortunate. It also likely happened because the transmission was on it's way out anyway.
At cruise with light throttle, the pressure from the linkage is barely applied.
I tend to agree with you regarding your second sentence but not the first one. If you are aware of how a torqueflight works you can absolutely drive one without the linkage hooked up and make it live. But under even normal driving scenarios, and an operator who doesn’t understand what the throttle pressure linkage does, without it the trans will quickly go away. My trans was rebuilt by a local shop about 2000 miles prior (and working flawlessly) before my linkage fell apart and killed the trans. I know when it happened because the throttle stuck, and I whacked the pedal, shut it down, opened the hood, fixed the throttle linkage, but neglected to notice the ball on bell crank back by the firewall had come off. I was a dumb 17 year old and had zero knowledge of how a torque flight worked. The guy that rebuilt the trans (and I tried to blame for the failure) quickly educated me about how important the throttle pressure linkage is.