A few thoughts.
First is that there will be some noise. No escaping it. A little bit of a groaning or howl that's not quite a growl is normal. You might notice it more when slowing down or driving down a hill where the governor is holding the tractor back so that you're riding on the back side of the gears. That type sound might also be noisier in one gear than another, which would generally indicate that the tractor got a lot of hard use in that gear in its working days (long days cultivating, as an example). Again, all perfectly normal, so a lot of it is the nature of the beast and no cure. If one gear seems noisier than the other, you could try finding different gears from other tractors that might mate up and be wuiter, but that's bit of a long shot. If that's the only kind of noise you're having, it is not a sign of imminent failure, and would take a lot of hit-and-miss shopping to cure. It will always have that certain groan to it. It did when it was new.
If you've got a clicking or popping type sound or a VERY distinct growl, that would indicate a bearing somewhere in the works that needs attention. And they can be the very devil to track down. Sound travels fast in iron. A sound that seems to be in your left ear where the tranny is could be originating in the right final drive. If could be a bearing, it could be a loose wheel lug. Patience on that, but they can be tracked down.
As far as missing a gear. It's not clear if you're trying to shift though gears or not. If so, forget it. The tranny is not synchronized. Pick your gear for what you're about to do, adjust your throttle, ease in the clutch and go. Unless you've got three arms (one for the governor control, one for the shifter, one for the wheel) you're not going to be able to reliably shift the tractor from gear to gear while in motion and not have some grinding. That said, there is what I call the Farmall grind. The gears in an A/B/BN tranny are straight cut gears, unsynchronized. Even starting from a stop can cause some grinding. Causes can be several. 1) When the input to the transmission stopped spinning the gears you choose next are not lined up, so you ease off the clutch to get things spinning and grind it into gear. 2) You might shift too soon after stopping. In this case, especially with a warm transmission where the oil is warm and thinned out, it won't stop the spinning of the gears. 3) It cold be as simple as a sticky pilot bushing. This is an Oilite bushing centered in the rear of the crankshaft of the motor that supports the front end of the driveshaft turning the transmission. If it's sticky, it will continue to transmit power to the shaft even when the clutch is released. Not bad to change out but it does require a split behind the motor and the tools to do it. Solution to try before deciding that anything needs fixing is to depress the clutch pedal and wait (You don't need to have a smoke while waiting, but give it five or more seconds) before selecting a gear and see if that doesn't cut down on the problem.
As far as splitting the tractor like I referred to above, or pulling the differential shafts (that transmit power from the diff in the tranny box to the final drives) or the axles (on center with the wheel hubs), the most important advice I can give is to have ample wood (not cement) blocking to support things as you work. Blocking, jack stands and bottle jacks. That's so nothing can fall. All completely do-able, but it may take some heavy wrenching coupled with colorful language to get things apart, so you want things to be stable. The manuals outline the differences between the right side and left that relate to things like the location of the brakes . . .
Which comes to your last question. If you're contemplating this kind of work, I'd recommend the complete set. First off is the Operator's Manual. This doesn't get into heavy mechanical work. It's maintenance mostly. THen come the tech manuals. You could probably get by with one or the other, but I've found it useful to have both the IH Blue Ribbon Service Manual for the A/B and the I&T IH-8. Either one would get you by. A lot of what's in the I&T is ripped right from the pages of the IH manual, but each has enough in it that the other doesn't that it's been worthwhile more than once to have both at hand. Final book for the library is the Parts Catalog. A great resource. Part numbers for proprietary parts, and for the most part, sizes for fasteners. The best use I've got of them is the blow-up, blow-apart diagrams that have got my carcass out of more than one jam in noodling out how things come apart and go back together.
HTH
Link is to a page from a website I used to keep up -- shows the rear of my BN apart.
Rear back onto my BN
