What does it cost to have the trans rebuilt at the dealer??
Typically less expensive than buying a complete re-manufactured unit because they are repairing the root cause of the issue and any affected components as opposed to replacing everything. A certified, experienced trans tech can tear down a 6R80, diagnose the issue, and re-assemble the unit within 1 day (assuming parts are readily available).
Here are some things to consider:
1. A clean, indoor shop. The transmission and it's internals should not be exposed to an outdoor or dirty environment.
2. A Ford specified transmission flusher. Dealers are required by Ford Corporate to have a heated transmission flusher with a 3-filter system, flow gauge, and hour meter. These flushers look like a small red colored air compressor (barrel design) and have red/blue hoses. The unit is made by a company called G-Tec. The flusher is used to clean out the transmission cooler and cooler lines; if they are not flushed or replaced the result is a repeat failure. If they don't have one, run, don't walk away.
3. A Ford OEM Certified transmission technician with experience. The tech should be certified in Ford Specialty 37 - Automatic Transmission. If the tech is not certified, do not trust them with the rebuild.
Hope that helps.