It appears to me that you have un-meshed your timing gear teeth and they are not re-meshing in properly, explaining the gap between your pump and the mounting face. Even if you can get it to mesh in again, there is a good possibility that the timing gears will be off by a tooth, maybe more.
You will have to pull the timing gear cover off to check the timing gear alignment marks (3 pair of timing marks.). If you want to remove the injection pump, the timing gear cover has to be off in order to get the pump drive gear off.
You need to get a shop/service/repair manual for your tractor. Ebay has a good selection of manuals for a 340A. If you can find an I&T shop manual, they provide less detail, but cost about $35. A manual will provide procedures and also pictures illustrating the correct setting for timing gears. It's not a difficult job, but entails a bit of work.There are 3 pairs of timing gear marks that you have to line up when reinstalling the pump.
Incidentally, the external CAV pump timing setting is normally zero degrees. Some mechanics set the pump timing for maximum power using a dynamometer, which explains the external adjustment. But they don't start as well with the timing off zero.
Hope this makes sense to you. If I can do it, you can do it! Post back with any questions.