First things first, as a Pro-Tip, you can stick a big screwdriver through the slots in the driveshaft and use that for leverage when installing/removing the cruciform. No need for the time/effort or risk of damage clamping it in a vice.
The selector rod threads look okay to me, albeit a little ugly. Nothing to worry about though, so long as the new cruciform is willing to thread onto them. Don't forget a little loc-tite when you install it, though.
Next thing I see is that I think what someone did is try to install a oil seal adapter
which lets you use a P-style oil seal with the older bearing design. CM2 did this successfully on his VBB cases, but he's Not Normal when it comes to these things (unless "has a 3-axis CNC in his garage" is the new normal around here
Also, you remove that seal by pulling it out from outside the case with a pick, though, not punching it in like that original seal would have been removed.
The more I look at that fly side case, the more I think that it could be set right by bolting it all together with a crank in it, chamfering that crack a little, and then filling it back in with weld. It'd be a total bodge, sure, but if it holds pressure and isn't structurally unsound, I don't see what the issue is. All the main force is on the main bearing, and that seat seems to be uncompromised.
Moving right along...they used a sealed main bearing, which I can't comment on, but I've never seen that done before with main bearings (I use them for my front fork and driveshaft bearings all the time). Maybe to help prevent/contain the leak around whatever Bad Touch was put on the fly side cases. Either way, I wouldn't do it there. That hole you asked about is a vent to allow mixture to get behind the bearing and lubricate it, btw.
For the main bearing, 99 times out of 100, if something is stuck on a Vespa motor, heat will be the answer. Having the correct specialty tool (in this case a bearing puller) also goes a long way to solving that problem. You can get a set of cheap blind bearing pullers at Harbor Freight or Northern Tool for about $50 that will be adequate to your needs for a long time to come, and honestly they're not materially lower quality than you'll get from SIP, just a hell of a lot cheaper. In the case of my main bearing puller, the HF one might be better!
I agree the piston looks okay...for definitions of "okay" that include an OG piston with 2mm rings.
I'm guessing the scraping is damage you did to it with soft seizes, but that's where those thick rings really shine.
The crank looks like it's seen better days, but unless you're certain you want to keep these cases, I wouldn't worry about it. If you *do* decide to do something, I'd swap to a P-cone conversion crank
so you have access to the full suite of modern ignition systems.
Now, then...the intake has been flowed for a 24/24 carb at some point, but the intake timing looks stock.
And, lastly, the wear on the cases looks inconsistent. Like, there's lots of oxidation inside the crankcase on the clutch side, but not the fly side. Are the cases a mismatch, or am I just overthinking here?
Anyways...that's what I got off the top of my head. Lemme know if you have more questions.