What I would do if I were you... start by hooking a ground wire from the alt case to some point on the engine block or mount so you know the alt has good ground. Then take a #4 wire from the BAT post directly to the Bat+ side of the starter relay so you know you have a direct connection to the battery. Make sure #2 is hooked back to the BAT on the alt and #1 is supplied battery voltage through the key or jumper or whatever so it's excited. When this is all done... start the engine and rev it to 2000 rpm or so... thus you know it should be charging. If it doesn't make 14+ V at the battery, get another alternator. If it's warranty... probably don't discuss this so much. Just install the new one as stated above.
For my own part I'd much rather see the exciter wire run through a 194 bulb from the key. Then you have a charge indicator light. Voltage is really the only measure that counts with alternators...
If you want to rehook the ammeter after all is known to be working... I would suggest you make sure and have at minimum a 60 amp meter... and wire it such that all of the tractor's electrical loads other than the starter are run through the ammeter... so one side of it is the main electrical terminus (including the alternator's BAT wire) and the other side goes directly to the battery pos at the starter relay.