Sorry I can't offer a wiring diagram, but can make a few comments that may help (all theoretical):
-the ammeter goes in series between alternator's one output wire and the battery. There's a positive sign on it; that side goes to the alternator.
-the regulator that is now on the tractor is just not used anymore, since the alternator has one built in. What was the field wire to the generator isn't needed, so just tape it up and tuck it out of the way.
-the wire from the key switch that now goes to "L" on your voltage regulator, can be connected to the positive terminal at the battery. It might be more convenient to hook it to the solenoid though, at the same place the battery positive will go (not the starter motor side).
-don't change your lights later, change them now or they'll all blow as soon as you turn them on with your 12v system.
-regarding the alternator pulley - you may want to use a slightly diameter than what's on the generator so it spins a bit faster. This way you'll get charging even at very low rpm. Because of the segmented commutator on generators, they can only turn so fast, which is why they barely charge at low speeds. -you haven't mentioned your starter motor. If you were trying to be perfect you would switch to a 12v starter. A less expensive way is to use a resistor in series with your existing starter, so it still only sees 6v. (The other 6 is dropped across the resistor and dissipated as heat). But lots of folks just leave the 6v starter as is, reasoning that it only runs for a very short time anyway so it won't likely burn out. In fact it might even run for a shorter time because it will spin so fast your tractor will start right up! If you are going to eventually switch to a 12v starter, maybe you can just wait until you burn this one out and do it then; it could be quite a few years.
Could tell us the model number of the alternator you got, or what car it's meant for? I would also like to do this conversion.