I have a 2006 JD 110 riding mower 42" deck with one blade that cuts higher than the other. It is about 3/8" and I already replaced the blades thinking maybe one was bent. Is there any adjustments to align the blades?

Hi,
I gather you mean an L110; there was a 110 thirty years ago. I can even tell you that your 13 digit serial number should begin with GXL110... It is on the tag that is above the left rear wheel/tire on the side of the frame.
That said the deck is adjustable side-to-side and front to rear, No adjustment is available if the blades, one or both have struck something solidly and warped the shell, a moderately common thing with the 42" shell in some geographical areas, mine included. To check for warpage, you must turn the blades so that they are end to end at the center if the deck and the blades should be within the thickness of the blades' metal of lining up. Check all combinations of this; one blade the same and both ends of the other. If they never line up, it is the shell. If it depends on which end, one end up and the other down; it is a spindle.
Remember that these blades spin in a circle so that the lowest part will be what shows.
Adjustment, if called for, is performed with pieces of 2x4s for the sides. Do it by placing two pieces one atop the other laid on the 4" sides on each side, four pieces total, two on each side. Drop the height adjuster to "3" in the gate on the left. With a 15mm wrench or socket/ratchet loosen the nuts on the brackets on each side about 1/2 to 3/4 turns, just enough to be able to move the black lift bracket on the yellow deck weldment; some had to be knocked lightly to free sticking paint. The black bracket should be downward as much as possible. Then tighten the nut to secure the adjustment.
Front is also adjustable by 15mm wrench by turning the nut on the "closed Y" shaped link. Hitting something with the front of the deck can bend the bracket that it attaches to below the front axle. Fret not as this bracket is available as a service part.
Peace,
Clarke

I can't give Clarke another greenie until I spread it around but he is right on the money here