John Deere 790 problems, won't crank?

I'm trying to help my dad find the problem of his tractor. He put a new fuel filter on his tractor a couple of weeks ago and now when he went out to crank it this morning, it cranked but when he stopped it and went to crank it again, it wouldn't start. Well he got to tinkering with it and it finally started. He bushhoged a little and it ran rough the entire time. Now he can't get it started. We have looked at the owners manuel and can't find anything to look for. It is a 2001 John Deere 790. It has 89 hours on it.