Hello and welcome to OCC!!
In the parts book, the pic shows an offset in the blade. The correct part number for the blade is 759-3939. Cub cadet only lists one blade, so if you want something different, you will have to look around. I hear a lot of people talking about the "Gator" blades. I'm not sure how they work with a bagger.
I'm not sure why the deck cuts so low. Perhaps something is bent. Or, the wrong blades are installed.
Baggers are temperamental things. The work on the principle that the air movement from the spinning blades will "blow" the grass up the chute. Personally, I hate them. I like my sweeper.

Here are some tips:
1.) They don't handle wet/green grass well, so make sure the grass is dry. (Mow in the heat of the day.)
2.) Because they "blow" the grass, cutting just a little off the top makes the clippings very small. The small surface area can't catch the air. (Imagine a full dead leaf, then smash it to pieces and see how well you can blow it.) Perhaps you need to let the grass grow longer.
3.) Too long of grass is too heavy. There is a happy medium.
4.) Get some graphite spray, and spray the inside of the chute.
Good luck!!