I have a 2006 honda 400 rancher canadian AT trail edition, which, like yours spent a long time without use. I bought it last fall with only 30 hours on it. It even had a mouse nest in the air filter. The bike just turned 1000 km last week.
When I used it the first few times, I did feel it was underpowered. Whenever I got stuck, it wouldn't even spin a wheel, instead it just moaned and groaned. I took it to the local honda dealer, they said it probably had the clutches stuck from lack of use and they "broke them free" when they did the first ever service on the bike.
Now, having used it a few more times, including a long hard run last weekend, it started to shift oddly, seeming to come out of gear a couple times when in difficult spots. Sometimes when its cold, it won't even move itself out of the garage, just like the brakes are frozen/rusted to the drums, even though the bike moves just fine when you push it. The engine simply seems incapable of moving the bike.
Today, when I was about to go out on the trail with friends, the bike wouldn't even move itself in reverse. In forward, it seemed to have no power whatsoever until higher speeds and higher RPMS. I oiled up the shifting linkage and after shifting it back and forth from reverse to forward a few times, I got it working fine in reverse, but again, in forward it had no power. I took it to a small hill, and once it was up to speed I could crank on the throttle and spin the back wheels, but from a stop, it still had no power. It won't even climb a small hill.
I'm going to take it back to honda, and it sounds like my problem is similar to the original posters problem in this thread.
My question for the original poster, is : How much did they charge you at honda to fix the problem?
Edit - I replaced the angle sensor and now it works fine. ($100 and less than half an hour work)