From what I've read, if its still got the gear indicator switch on the end of the shift drum then ditch it and when you put the bolt in shim it up with washers to make sure it has no movement. Loctite that bolt and the shift star bolt/screw on the other end. Make sure once the cases are back together the is no play in the shift drum from side to side. Some guys have deleted the centre case gasket, will close it up 0.4 - 0.5 mm and just used a smear of liquid gasket(like permatex aviation sealer). Me, I'd get a couple of centre gaskets from pit bike shop (my local shop sell them for about 8 bucks for a full set. Put it together, shift drum bolt in and torqued, and check it for side play. I clamp the cases to the bench and check it with a dial guage, if it had more than about 0.01"/0.25mm side i would buy a shim 0.05"/0.125mm to 0.01"/0.25mm thinner than the play. Most bearing shop, Enginering suppliers/specialty bolt shop sell shims in 0.05" increments, just measure the shaft diameter and get a shim with the same internal diameter. In saying that, if both the drive and driven countershafts had the same amount of excess play too i would just delete the centre gasket.
Obviously run it through all the gears by hand and confirm all is ok before going any further.
It seems that a lot of the zonger g box problem are down to that shift fork (which only affects 2nd), if theres play or wear it doesnt fully engage and when it skips ypu can hear it clicking, sounds like the chain is skipping on the sprocket.
Like i said, never opened up a big zonger but seeing your pics, your shift fork wear explains why 2nd is not engaging. Before digging too far into it, get you new fork or complete shift drum, make sure that fork is tight on the shift drum, if its not tight on the shift drum no amount of shimming will fix it at all. If it is all good, bolt the cases back together and go from there.