Sounds like you're wired up right and if you haven't already, this would be a good time to run through John T's list. If that indicates that you are charging but the ammeter still shows a discharge, it may be as simple as having the wires crossed on the ammeter. Are + and - labeled on yours? That's only a fix IF testing otherwise shows that you are in fact charging. If not all you'll have done by switching them is to have your ammeter show a charge while you're still discharging.
One little glitch that's a long shot but worth mentioning, especially if you show a charge with the wire from the F post on the generator grounded to the frame but not otherwise.
My BN did something similar to your tractor. It would charge with the four-position switch on H, but not on L, and I ran it down to the field resistor being bad. All it is is a fine wire wound around a fiber strip. The wires are supposed to be connected to the hollow rivets that secure the strip to the back of the switch body. On mine, the multimeter showed no continuity between the two rivets. Hmmmm. Testing the winding between the rivets did show continuity. Taking it one step further, there was continuity between one end of the winding and the rivet on the other end, but not testing the other direction. Though it looked good to the eye, one end of the winding was not making electrical contact with the rivet. I fixed it with just a drop of solder. Worked good after that, in fact had me worried as it made for a lot of smoke out of the electrical box until the residual crud burned off the resistor. Had me quite excited there for a few minutes!
If it should be the field resistor that is making your problem but you find it not to be reapirable as easily as mine was, you could rig a new resistor (Radio Shack) in its place. I can't find it in the archives, but one of the guys might be able to chime in with the specs for the replacement.
As a last resort, if testing shows your relay to be bad try cleaning the points in it before throwing it on the scrap heap), OEM sells replacements. You could also switch over to a regulator (as opposed to a cutout). All that would do is take away the fuction of the L/H positions on your switch. Either of those options will be easier and less costly than cutting up your hood to make room for an alternator and converting to 12V.
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