you are correct about the coupling separation but that will not eliminate the load placed on the motor from pulling the weight of the tractor and the load put on it by the HST during driving . But it will be a good for a static test.Timing is changed by shims between injector pump and block mounting surface. I don't recall if adding shims retards or advances timing.
To eliminate coincidental problem take shaft apart again, may be difficult but then you will isolate or eliminate that system as a trouble spot.
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Is this a good product ?
http://stanadyneadditives.com/injector-cleaner/