Thanks for the suggestions. I'll look to see if something is bent. I checked the length of the arms and they are the correct ones for the 46" deck. I think I incorrectly identified the deck as a 48" but should have said a 46". The 48" is the one I could upgrade to if I could find one.
As far as the PO doing something to mess it up, I doubt it. The most the PO did was take it to the dealer, which he did regularly. I would hope the dealer did things right.
I know the height adjust at the rear sets the height, not the wheels. If you look at the label though it states if you want your cut at 2" set the wheels in a specific hole and then set the deck height so the wheels are 1/4" off the ground. I know most WFMers say to go with 3/8" instead of a quarter. My issue was that if you put the wheels in the 2" hole and then set the height, the blades are actually well over 3 1/2" off the ground. Thinking about it, I wonder if my front anti-scale wheels have been changed as I mentioned the rear wheels were close to an inch off the ground... jdparts lists a gauge wheel kit but I don't know what the difference is.
kb: Things haven't worked right since I've owned it, but as I've only mowed with it a few times I wouldn't put much stock in that fact.
Kurt: I've seen those gauges and wondered if they were any good. Perhaps I'll pick on up the next time I'm near the dealer.
Last fall after I purchased the tractor my initial suspect was dull blades but the blades I got on my deck were actually brand new.