Blades are cutting at different heights what is wrong It's a scotts 42 in cut 17.5 kohler motor

Hi,
It can be one of two things, bent blade(s) or warped deck shell. Always easiest to work on with the deck removed. It is covered in the manual at:
Scotts Lawn Tractor Operator's Manual | ManualsOnline.com
And look for a pop-up menu near the bottom and one of the six choices is the Save option to capture it on your machine.
Rotate the blades to see how badly they line up when aligned; check both ends of each blade with respect to the other side. Blades may solve it for you, but the 42" deck is very flat and can warp, usually on the right blade side. For small amounts washers as spacers may work. For bad bends a shell or the use of a large hydraulic press on the old shell might be needed. Badly warped shells are generally visible as cocked spindles, cracked metal or paint chipping off where the spindle mountsto the shell.
Peace,
Clarke