Looking at the wiring diagram, there is one wire from the battery to the ignition switch. With the ignition switch off, there should be no other connection to the battery. That is assuming there is no problem with the switch itself. That is a possibility though, especially if it is stored outside or water has entered the switch causing corrosion across the terminals.
The best test for battery drain is with an ampmeter. Most multi meters have an amp setting, usually have to rearrange the leads, set it on a low amp setting and be careful not to over amp the meter. To test for draw, disconnect one battery cable, connect the leads in series from the battery terminal to the disconnected cable. The meter should show 0 amps. To test your connection, turn on the ignition switch (do not try to start), the meter should read the amp draw. Turn it back off, the reading should drop to 0.
You can do the same thing with a test light. Connect it in series with a disconnected battery cable, the light should not glow. This only works with simple, non electronic circuits though, which yours is, so it would be a viable test.
From reading the post, I suspect you may have more than one problem. The battery sounds suspect. Take the battery back where you bought it and have it load tested. That will tell if it is a good battery. It will need to be fully charged to test it.
Another possibility is the charging system is not making enough amps to overcome the amp draw of the PTO clutch. Looking at the diagram, the charging circuit feeds to the ignition switch with a red wire to terminal L of the ignition switch. With the engine running up to speed, and the PTO on, and any other accessory on, check the voltage from the L terminal to ground. Then check the voltage across the battery. They should be both the same within a few tenths of a volt, and should be up around 12.5 to 13 volts.
If the reading at terminal L is higher than the battery voltage, the ignition switch is bad or there is a bad connection in the plug.
If both readings are the same, but lower than 12v, the regulator or alternator winding is bad.
Try turning the PTO and accessories off, engine running at speed. If the voltage comes up to 12.5 or so, there is definitely a charging problem.
You said that after running about an hour the engine will not turn over. Is that a very slow turn, as in a low battery, or no response at all?
If there is no response at all, that sounds like a safety switch. If it is a slow turn, and the battery checks out as good, could be a starter problem. Check the side play in the upper bushing, could be the starter is dragging when hot, pulling too much current.
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