I'd start with a carb clean and adjustment, new spark plug, air filter, and an oil change, if all of those haven't' been recently taken care of. These motors are not very powerful to begin with, so any small item that can be fixed will help. The recall on the Hondamatic's in the TRX400AT bike was for incorrect swash plate angle at LOW speeds, under 8 mph if I remember correctly, so I doubt it has anything to do with that. Other things that can affect your top speed include:
-tire pressure
-alignment
-brake drag
-wheel bearing / cv axle drag
-your weight
-any other modifications to the machine that affect its aerodynamics or weight
Where are you located and where did you buy the machine from? Your pictures are blocked on my work computer because it says the link leads to another country. It's possible machines from countries other than the United States have electronic limiters on them.
I used to own a 2004 Yellow 400AT and it was a great machine, I had the recall done and it actually CAUSED the problem they said it fixed, so I had to have them do it again. After that it was sold unfortunately. However, even with the transmission acting up, ALL gears worked in ESP and only in Auto mode did it shift up too early and bog down, which is what the recall fixed (the second time for me). I don't remember what the top speed of it was, but I know it was quicker than my 01 TRX350FE which I have seen 50mph on. It takes a LONG time to get there though, and if there is any grade at all, it won't go that fast. I'd imagine the 400AT is right around there on a completely level surface with an average weight rider on it and in good running condition.