Is this possible at this time? I used megui to do it and the processing time was around two hours! WTF? Is this just how difficult it is to process DTHD? Have I not encoded correctly?
You don't give enough information for an answer. Did you convert the audio with the HD Stream extractor? Did you only convert the audio or also extract other tracks?
If you have eac3to, and NeroAacEnc in the same folder, you can use: eac3to audio.thd audio.m4a -quality=0.45 (default quality is 0.5, valid values until 1.0, less than 0.32 make HE aac)