Hang in there! It took me 2 full weeks to be sure I liked my Advantage and that I could be productive with it. It was like you said: I got used to the matrix layout as such quite quickly, the challenging part was getting used to the modifiers, new position of arrow keys, new position of common keys like Backspace, Enter etc. You use these without thinking, and during the transition phase you have to think about their new location, which feels like a step back. There's nothing but keeping at it though, in time you won't have to think about it any more, and (assuming you agree that most of these changes are for the better, if you think about it) eventually you'll be better off.
It's very similar to learning a new (software) keyboard layout BTW, only that is much harder.
Bear in mind I've only used the TE for quarters of an hour at a time so far, but I do believe it can work well (as others have attested), and I will give it a serious try at some point.