Killer_B:
The manual covers side to side and front/rear leveling but here is a quick list of what you do for side to side.
The biggest pain is you need to measure the 'blades' when they are sticking straight out to the sides. The deck has no alignment guides (Would make it too easy to level - I may weld some on sometime).
First, turn off the tractor, disengage the front PTO - you'll be turning the blades.
Drop the deck to your cutting height onto the stops - Make sure the wheels aren't touching.
Measure the blades from the floor (A level floor of course) when they are straight out - you'll probably need to turn the blades between measuring sides. If they are more than 1/8" off (or even less) you should adjust them. To adjust them
look at the back of the deck, you'll see two (one on each side) yokes with rings in them. You can either lower the high side or raise the low side but if you raise the low side make sure that when it's at full raise it doesn't hit the stops or anything else. To lower a side pull out the ring and clevis pin, and loosen the turnbuckle. Unless it's way off I always go just 1/2 a turn then put it back and check the blades again.
That's it in a nutshell. I hardly ever have to adjust the front to rear level but if that's more than a small amount off (The front should be level to a tad lower, never higher than the rear) you should adjust it. Take off the front mount and do the same with the turnbuckles on front. Tightening them will raise the front of the deck, loosening them will lower it.
Note, you'll be on your back and reaching doing this. Probably cursing a few times also...
To measure the blades on the non-discharge side is a pain unless you get a little gage that JD sells for less than $10. It's still a pain but a little easier after you do that.
You could probably get close to level by measuring the distance of like adjusted anti-scalp wheels in the rear and front but I've never tried this and it would be as accurate as measuring the blades.
Also, on the Height adjustment knob I think 1 rotation (6 clicks) is 1/2 and inch in height) having no marks here is a little bit of a pain.