You've started out great with the right steps in mind. But here's the thing---you did get him used to staying in with the door open with you away, and with it closed for long periods of time. What you may not have covered is the in between.
Have him enter the kennel on command, click and treat. Since he's already got this down, you won't have to do this more than a few times. Then, push the door to, open and click and treat.(If you've already done this and slowly increased the time the door is closed, then start increasing your distance. Shut the door and stand up. Kneel back down to click and treat.(Repeat, repeat....) Shut the door, stand up, and take a step away. (Repeat, repeat...) Shut the door, stand up, take a few steps away. And so on...
Another thing that could help him is if you worked on longer distance stays from the kennel. This kind of makes the whole thing more of a game. For best effect the door could be pushed to or completely open, either way. Probably pushed to just so that there's still a "barrier" between the two of you but when you call him he can still happily push it open to head your way. If you've been trying to slowly increase your stances already, perhaps he needs smaller increments. If he gets yippy during training---Oh darn, the game's over. And off you go to do things other than play...but just for a minute or two. Then, "Oh look at the puppy! Back to work..." And the fun begins again. Or you can try using the quiet command if he knows it yet.
He may just be testing you. If you've tried these things, disregard. ^^ Many dogs will resort to vocalizing when they get frustrated trying to learn something--this is how most people recommend teaching speak, as I'm sure you've heard. It's their last resort--fine, I'll try this!! Maybe try clicking for less of a try. For instance, if you're wanting him to step on a box(which you've already done) don't wait for him to get frustrated when he doesn't get it. Click for stretching in the direction you want. Click for leaning forward. Click for little tries, rather than something closer to the end result. If he gets frustrated easily this is the best way to go.
Hope this helps!