I can provide some input here. Either one, or all of the below fixed my very similar problems discussed above:
1) I replaced the TC motor. I adjusted the torque spec to the required 89 in. lb. on all 4 bolts (i think this is critical)
2) I would suggest this to everyone. REMOVE the IWE system all together (Even you Gen 2ers). I understand that it may cause minor premature where, but Ford is the only manufacturer with this system to gain as little MPG to appease the EPA (to my knowledge). The system is garbage and needs to be gutted. (I suggest RCV rings for this $150/pair). 1 hour job if you are mechanically savvy at all.
3) User Operation and sequence of engaging 4L is critical as well. First come to a COMPLETE stop, even letting the motor and gears to spool down completely while in neutral. Second, shift in to neutral (if the cluster indicates "shift delayed, pull forward" DO NOT shift to drive as this confuses the system. Give it a few seconds to engage, and lastly and most important DO NOT depress the brake at any time as this will also disrupt the sequence and it engaging properly. Yes you will hear a slight "clunk" when engaged, this is normal. Follow the same procedure to disengage.
Hope this helps someone....