Thanks all.  Yes, I had one too many zeros in my break-in time.  Its not 500 its only 50.  And yes you're right, the LS owners manual does not indicate a break in time.   My dealer only mentioned the required break-in period for the first 50 hours when he dropped off the unit but did not furnish the engine owners manual.  Interestingly enough, Mitsubishi does require a 50 hour break-in for the S3 series industrial engines.  I have found a few different versions of the S3L manual (engine on the J2023H) and they all have a short paragraph that states, "Break-in the engine: To break in new engines or overhauled engines, operate the engine at a speed lower than the rated speed in a light load condition during the first 50 hours of operation.  Operating new engines or overhauled engines in a severe condition during the break-in period shortens the service life of the engine."
Jack,  The top of the gearbox is directly hitting the cruise control linkage when the deck is raised.  I talked to my dealer today and it turns out the cruise control is a separately boxed kit that is delivered with the tractor to the dealer and they must install it.  It is not factory installed.  I am having my dealer stop by to take a look at it and make any adjustments needed.   I am not going to mess with it right now as its under warranty.  They did indicate that the unit they have in the showroom works fine so I think its just an adjustment issue.
Thanks again everyone.  I am liking the tractor so far.  It seems pretty durable and with proper maintenance should give me years of trouble free operation.  I hope you all feel the same way.