I should have included that, the transmission ran fine before the engine swap. It had new filter and fluid about a year ago.
The way that I look at it is the engine came out so the linkage was unhooked and the engine separated from the torque converter / trans. Could the torque converter itself be causing this.
Sounds like either the converter took a dive or the pump did. I would pull the trans out, tear it down and inspect everything. Rebuild with quality parts with new quality converter and reinstall. You will be glad you did.