Yes, it does sound like a restriction somewhere in your fuel supply line. I would trace it back as far as you can and look for kinks or pinches. It could have sucked up something, you may be able to clear it through a careful application of some compressed air. Do a visual inspection first. Avoid blowing compressed air through the fuel filter.
As far as break-ins go, there are various opinions. Some say to not run the engine at full speed or full load for the first 20-50 hours. Any engines that we have rebuilt, we typically just operate them at constant rated speed and full load. I have seen too many engines get babied after rebuild, and then end up burning oil because the rings never seated properly.
Have a look at your operators manual for what Deere's recommendation was for when the machine was new.
HTH.