I took it to the dealer and they "loaded" an update, but when i got it back, it still showed the old version 4.27.12058 a.k.a. 3.1.3. Mine has the warranty extension 12M02 for the APIM, but we haven't really explored that due to the fact the unit is still functioning. They won't replace it under 12M02 unless it's dead or throwing a code.
Took it back today and spoke with the technician. He seemed genuinely interested in fixing it (which is a refreshing change, btw) and when we looked up the TSB on his computer, we found a flow chart that basically asked "What is the last 5 digits of the CCPU version?", and if it's not 15128 (a.k.a. 3.8), apply the update. He seemed genuinely surprised when I showed him it was 12058 (a.k.a. 3.1.3). So once that happened, he realized that there was something not right, admitted that Fords can be hard to update sometimes, and asked me to bring it in.
Of course I agreed, knowing full well that the road to getting the Sync/MFT updated on this thing might be tough. But if I'm going to keep this thing for the foreseeable future, I want it working right, or at least as "right" as Generation 2 Sync can be...
Thanks for the feed back, all!