Your first problem was definately the converter. The second issue is a known problem wit hthe E4OD and R4100 called the shift flare. There is actually TSBs for such. The fixes are all electronic in nature, like changing the pcm program. I have a valve that was manufactured to completely remove the shift flare. It is a problem in the valve body.

Although, it would fix it, I would prob let them change the transmission anyway due to shrapnal blown thru trans from TC. That's what happens when they are going out. I think they are being a little hasty as they could rebuild valve body and install a line filter as Ford requests on the TSB bullitins.
Bob