A pump with a worn head & rotor assembly will usually result in a tractor that starts fine cold but will NOT start when hot (not the converse).
An engine with poor compression do to cylinder/piston area wear will start poorly cold and BETTER hot.
Going by what you've already stated - you've got a pump with a new head & rotor installed, yet the pump guy did not install the static timing marks? That's sounds odd.
You didn't mention engine cranking speed. I mention it since it's often a prime issue with just about any modern Deere. The closed-center hydraulics often result is poor hot cranking - and that results in poor hot starting. Thus the utility of a $10 pump destroker.
Also, as another poster has mentioned - if the rocker-arm adjusters on the valves are too tight - the engine can start well cold, but barely start at all when hot. More common in gas engines suffering from valve-seat recession - but it happens at times in diesels depending on the quality of the last valve job.
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