1940 Farmall H transmission Gear Removal

Several teeth missing. Tractor is split in half at the transmission. Removed the covers for the front upper and lower bearings. Now, I am trying to figure out how to remove the upper and lower gears from the shaft and the transmission case. The upper shaft is very loose but there is no way that I can remove it without removing the pinion gear going to the ring gear of the differential. The lower shaft is loose, and it extends back to the PTO shaft.
How do I separate the bottom shaft to remove the bottom gears and allow (maybe)the removal of the gears on the top shaft.

Split at the transmission means the center housing is not attached to the transmission? If so get the top off if not already. Remove the transmission input shaft housing with shaft and bearings at the front of the trans case. Take the 3 bolts from the main shaft bearing retainer (top shaft). Slide shaft with gears forward and tilt and lift out. Pilot bearing and gears can be removed from it. Keep track of the shims to put back. On the bottom shaft with trans top off, slide two gears engaged before removing the top shaft to lock the countershaft from turning. Loosen the slotted drive dog at the front of the counter shaft. Just leave it on until later after loosening. Remove the left and right brake linkage. Remove the left brake lever on the clutch brake cross shaft. Remove key and clutch pedal. Slide the cross shaft to the right until the end clears the countershaft rear bearing. Remove the bearing retaining ring from the rear of the counter shaft. Drive the rear bearing off the countershaft and from the housing. Finish removing the slotted nut on the front of the shaft. Remove the front bearing retainer then move the shaft to rear out of the bearing. Maneuver shaft out of the housing with gears. Gears are a press fit on the countershaft.

This was the question that I have. You stated that; "Loosen the slotted drive dog at the front of the counter shaft". The slotted drive dog, does it unscrew? Clockwise or counterclockwise?

Yes threaded on. Regular right hand threads, if looking from the front of tractor to the rear it would turn counterclockwise.

I have the upper shaft and gears out. I have removed the brake shaft and the dog in the front. I have the shaft moved to the back, but the rear bearing is extending into the transfer case. Does the rear dog screw out to release the rear bearing? Because, I still do not have enough room to clear the front shaft from the front of the transmission case.
Sorry for being so naive. I use to rebuild cars and have rebuilt all kinds of engines, lawn mowers, V4s, a V6, a Mercedes Diesel, a Corvair 6, and 3 V8s, but I have never worked on a transmission. Especially a tractor. Fortunately, it is not an automatic. Thank You for your excellent assistance, and your patients.

There is a snap ring that has to be removed before the rear bearing will come off the shaft. I have removed them before and yes, it is a PITA... Once the bearing is off, the shaft will come out.