Hobby Horse put out a book on how to use their press. The first edition had a green cover. The second updated edition had an orange cover and came out under the Lionel name. It was the instructions Lionel sent to their service stations, but it was written by Hobby Horse. You should start watching eBay for one of these books. In most cases the wheel cups control how far the the axle extends beyond the hub of the wheel, so measurements to get proper gauge is unnecessary. This is true for post war, prewar requires that you watch out for proper gauge. Best thing to do is measure back-to-back dimension prior to disassembly and check it after reassembly. Working with diesel wheels does not require quartering, which simplifies the job. Normal practice is to pull the wheels without the gear. The geared wheel is left on the axle. In most cases Lionel sold the gear side wheel with the axle mounted as the replacement part. For the center worm wheel, press the geared wheel and axle through the worm wheel in the center gear box. I then use thin brass strips between the wall of the gear box and the worm wheel to get it centered. One thing to watch out for is frequently the wall of the gear box has draft. If the axle is pressed onto the worm wheel against this angled gear box wall, it can cause the worm wheel to go on cocked. To compensate for the draft, tapered shims may have to be used.
I like to have an interference fit between 0.0015” and 0.002” for the axle diameter and wheel or gear bore, not including the knurling. If the interference is greater than this I use hand reamers on the bore to get the proper interference. If the interference is less than this, I use Locktite 640 to hold the fit. When the axle is knurled in the center for a worm wheel, this knurling has to be pressed through axle bearings mounted in the truck frame, usually scoring them. Lionel, on some applications, avoided this by slipping the bearing on the axle before pressing the geared wheel on the axle. This then requires that the bearing be pressed into the truck frame at the same time as the axle is being pressed onto the worm wheel in the center of the truck. This can work, but it must be done slowly to insure everything is lined up properly as the pressing occurs.
For bearings, I like to have 0.002 min. to 0.005” max clearance between the axle and the bearing. To press the bearing into the truck frame I like 0.002“ interference, but a little more than that will also work. The bearing bore can be reduced by the interference in the truck frame, so it is best to check and adjust the clearance after the bearings are in place. Most post was bearings are Oilite, which should not be reamed to avoid closing up the pours with the oil and graphite in them. If clearance adjustment is required on the bearing bore, files or abrasive paper can be used to correct the clearance. Solvents are not to be used with Oilite bearings as it will strip the oil out of the bearing. To clean up the installed bearing, rinse it out with light oil. Since it is not possible to check or adjust the bore of bearings pressed in already installed on the axle, it is best to have the bearing clearance on the large side with this application.
For wheels which do not fit tightly on the axle, get one of the Locktite products that is not runny. I do not recall the number right now. Then apply grease on the axle at the bearing fit to keep the Locktite out of this location. The rim of the wheel should not rub the truck frame. If it does, shim this location by putting one or more hardened washers, part number 671M-23, over the axle between the wheel hub and the truck frame. Locktite products need to be applied after the parts are cleaned with acetone. The Locktite primer should also be used. For the tools and other products needed to press wheels, I purchase from Mc Master Carr. Jeff Kane, The Train Tender, is a Hobby Horse dealer and is an experienced wheel presser.
it sounds like a lot of detail to press wheels and gears, but after doing a few, it becomes fairly routine.