Boy howdy you are new to this aren't you.
1. stick transmissions don't have "pans" like automatics do.
2. I think that the guys explained it but the shift pattern you "thought it should have" is for a 4 speed and not a 3 speed.
3. Looking at this, I think that is a stock transmission, Maybe not the "original" transmission but a stock for 58 transmission. This guys has one similar for sale and you can see he casting numbers on the pieces that you might find on yours
https://www.ebay.com/i/401678700304?...3D401678700304
4. that particular shifter was a "universal" shifter that they sold for under 30 bucks in most places in the 60's. Great for hanging up and breaking a trans but not very great for shifting. Universal meant that they sent along instructions on how to bend the rods so they worked right with the various transmissions you might stick them on. It looks a whole lot like the Spark-O-Matic shifter I bought for 17.99 for my 51 Mercury when I was 16 and had broken the column shifter. In truth you either need to invest in a far better quality shifter or invest in repairing/replacing the column shifter.
No matter if you plan to keep it stock and just fix what needs to be fixed or restore it or go full tilt and swap engines and do updates I'd suggest ordering a factory service manual for the 58 truck. One like this reproduction of the originals that were used by the mechanics in the Chevrolet garages when the trucks were new.
https://www.ebay.com/itm/CHEVROLET-1...U7Io:rk:7:pf:0 Those were written in very basic language with compete instructions on how to do a task. With basic mechanical skills If you can read and comprehend you should be able to do the task.