1998.5 24 Valve Cummins only runs with OBD2 Scanner connected

[Daletec]

I know it sounds like a grounding issue, but could this also be ECM/PCM related?

 

[BossHogg]

It has the smell of an unbalanced network. I don't know what network topology they used back then but if they used a network like CAN, that is a dual wire balanced network much like ethernet. Endpoints of the CAN network use 120-ohm termination and if that termination is missing or there is a broken/corroded network wire, that could cause excessive message errors. Your tool is likely adding a balance to the network. Just my guess.