The proper way to upgrade from Sync 3 V1.x is to upgrade to Sync 3 V2.3.x and then to Sync 3 V3.0.x. This is not explained on the Ford website, and they don’t even offer the files to do this anymore. The voice recognition issue is one of the results of skipping thru the versions. But you didn’t know this, that’s ok.
Since your APIM seems to have finished the upgrade to 3.0.20204, it could need a master reset. This is mandatory after any larger jump in software or firmware changes.
SYNC® 3: How to Perform a Master Reset | Ford How-To | Ford - YouTube
Even if you did this after the upgrade, do it again…then run the APIM Interrogator Utility and post the results here. You will use the GB5T-14G386-AA or GB5T-14G386-AB file mentioned in the tutorial.
Tutorial: APIM Interrogator Utility/Create Interrogator Log - Ford / Guides - CyanLabs Official Community
Where did you get the upgrade files for this and who’s instructions di you use? It certainly made a mess out of your Sync system. Fortunately, it can all be fixed.