The powertrain warranty from Ford is 3yrs/36,000 miles unless you purchased an extended service plan. Also, with Lemon Laws, you'll need to check your state laws. In Wisconsin, the dealer can make four attempts to fix the same problem. Since this is a different problem than the engine, it wouldn't qualify. Still, your state may be different, so check with your DOT.
You could try explaining what's going on and likely someone here will be able to help you at least diagnose the problem. If this is the same place that has replaced your engine twice already, my only advice at this point would be to find a different shop.
