I'm not familiar with that model, but it shares some things with others, so I'll attempt to provide some answers
1. The zerk (grease fitting) is listed in the New Holland parts site as "Quantity 4", so you do need the bottom one on the right side. The picture in the part detail looks like it is a press-in style rather than a screw-in style. It says that it's 1/4", so you should be able to use any generic 1/4" press-in zerk.
2. I can't tell from the photo of your front wheel whether that cone in the center is a separate piece that's supposed to come off or if it's part of the hub that the wheel mounts to, but it's not in the parts diagram for the front wheel assembly, which includes the hub. The parts diagram looks like the picture from the manual that you posted next to the photo of your wheel. I would jack up one front wheel and remove it to see whether that center cone is part of the hub or if it's something attached to the wheel before I tried to remove it by force. Be careful though, as the front tires may be loaded with fluid for ballast, and even 16" front tires can be very heavy if they're loaded with fluid.
3. The blank plates in that picture from the manual look like they're from a tractor that doesn't have a 3 point lift hydraulic system or PTO, and the photo of your tractor looks like you do have 3 point hydraulics. The lower plate in your photo matches the insert in the parts diagram that is labelled "WITH TRANS. PTO LESS HYD. PUMP", and in that case the level check plug is the one that you are calling #2 in your photo, the lower, more forward plug. It is close to the same place as the one on my 4000, and it's a pain as you have to remove the foot rest to check the fluid level.
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