I managed to get the pump off. This style pump you have to pull pump out and the gear stays in.  It is keyed so will only fit one way.  Service man said mark the gear and case to make sure it doesn't shift.  The other style pump he said the shaft stays with the gear and the pump is pulled off the shaft.

It is the 2nd cylinder that pumps.  I even tried cracking the lines at the injectors to see if it was maybe an air lock somehow.  It still only sprayed from that line. I have injectors removed also. When it ran it seemed to only miss on one cylinder.  We perked it and now it wont start.  Right before I removed inj pump I tried starting again.  It had been inside heated shop for 4 hours AND plugged in.  Engine was very warm to the touch.  It still wouldn't even pop, not even the one cylinder.

This tractor also cranks over too slow when cold.  We have tried new batteries and cables.  Only thing left is the starter, correct?  You can put a charger or jumper cables on it and it still only turns over at half speed.  Sometimes it will crank fast but not often or for long.  Battery is Deere and a year old or maybe 2.