Oof... I hadn't thought of the selector rods. Unfortunately they do look different to me:
FWIW, there is no tool for keeping everything together when removing the bearing carrier except your hands.
Engage 3rd or 4th gear and reverse at the same time to lock the transmission internals. I would do it by pushing both the top and bottom selector rods forward. Note that you can't lock it in 1 or 2 (middle selector) and any other gear at once, it should be physically impossible to move two neighboring selector rods at once.
Remove the pinion shaft nut (the top one, which should be left-hand thread), loosen but don't remove the layshaft nut (the bottom one, which should be right-hand thread), and remove the drawbolt from inside the layshaft (right-hand thread).*
Remove the 9 nuts holding the bearing carrier in place and put the box back in neutral.
Slide the bearing carrier away from the case while supporting the pinion shaft gear stack -- the layshaft gear stack should remain on the layshaft.
Tip the assembly so that the gears are up and the nuts are down. Support the assembly on 2x4s (the cheap, aggravating way) or on a purpose-built stand such as Pegasus Auto Racing Supplies part # 1409.
Remove the layshaft nut the rest of the way and pull the layshaft upwards to remove it from the layshaft stack.
Lay out all parts in order, noting which direction everything faces and how the shift forks mate to their dogs.
Reassembly is the reverse of removal... except SO much more aggravating! We need a tool to line up the splines on the pinion shaft stack and hold the stack in place, but no such tool exists (partly because the pinion shaft is larger OD than the ID of the rear pinion shaft bearing). Oh, and try not to get the sealant all over your hands at the same time.
* The purpose of the layshaft drawbolt is to keep the clutch shaft engaged to the clutch shaft to layshaft coupler sleeve when you pull the gearbox from the engine. When you reassemble, the torque spec for it is "finger-tight, then back off half a turn." With the gearbox not mounted to an engine, it's likely that the coupler sleeve will disengage from the clutch shaft. You can try to prevent it by pushing the clutch shaft towards the back of the gearbox, particularly when reinstalling the bearing carrier and screwing in the drawbolt. If the coupler sleeve falls off the clutch shaft, you will have to pull a side plate to reinstall it. OTOH, I think you'll have to pull a side plate anyway because you'll have to flip the ring gear/diff when you flip the box.
Resetting the selector rods is easy for very experienced hacks but a little iffy for novices (I've never had the guts to try but I watched it done entirely by feel in about 20 minutes, no setup jig or gauges... and then I set a track record with it!) IF the selector rods can simply be rotated, you shouldn't have to re-shim the forks. But if you have to replace them, or move the Reverse rod to the 3/4 position, you may have to have them re-shimmed. Of course, the spirit of Mike Hewland could smile on you that day... maximum interchangeability with minimum fuss was his goal!
I'll be interested to know if the top selector rod engages 3/4 or if it engages reverse. Trying to do the math/geometry/geography of the current setup, but I think that would have to be the case. Which would mean that the top selector rod would have to be moved to the bottom, the bottom to the top, and the middle flipped. Now I'm trying to picture if that means new shift forks...
Oh, and... I speak above assuming a 4-speed configuration. I believe FSV was allowed 5 gears, which means that when I say "3/4" it would technically be "4/5" and when I say "reverse" it would actually be "1st/reverse".