Well, I'm a newbie to tractors, but have had some experience with diesels.... Timing on the injector pump is pretty critical; if it didn't get put back precisely where it was (from a rotational perspective), it will create problems. Did you mark it before you removed it? Is there a notation as to position in the manual? It may be possible to "ballpark" it by rotating it a tiny bit and trying; typically, setting injector pump timing by the book means disassembling the entire front end to line up all index marks on drive chain sprockets, much the same as for replacing a camshaft or timing chain/belt.... Hope this helps.