Just an update, I removed the deck last weekend, replaced the bearings in all 3 spindles and replaced the belt. Took all of 45 minutes to remove the deck, rebuild the spindles, put the deck back on and level it.
The 46 inch deck seems to hang much lower than the 42. My guess is the 46 seems to be a fuzz deeper than the 42. Which with all being equal, would cause the 46 to be closer to the ground in all positions. No big deal, just had to make some test cuts to figure out what notch to mow in.
I believe I am done messing with it for this season.