On mine, thankfully the hole lines up nicely when it's folded all the way back. Looking at yours, it seems like the thumb is floating compared to the stick, so I can see how that would be a pain. If that was my machine, I'd be welding additional tabs on the top of the thumb that would hit the stick when retracted, and the tabs would line the pin up when the weight of the thumb is resting against the stick. If the machine wasn't mine, I would use a couple pieces of 2x4 on edge between the stick and the top of the thumb to hold spacing, or I'd run a chain all the way around the back of the bucket, over the teeth, and use the curl of the bucket to hold the weight of the thumb, and adjust as necessary by curling until the holes line up.
Bunch of ways to do it, but the common theme is to use the strength of the machine to help you.
I frequently just leave the thumb down but on the highest position when I'm working, it allows you to dig but still have the thumb there if needed, which is nice for the type of work I'm currently using it for. The lower pins are better if doing a lot of thumb work. The higher up you pin, the further you need to reach from the machine to grab something. So the highest pin location is a compromise, not great for digging, not great for thumb work, but it does alright at both. If loading a truck or doing a lot of pure digging, getting the thumb out of the way is nice. Not sure if this was a one time thing for you, or if the machine will be there for a while. If you'll be using it more, it would be nice to get the process so it's quick and not as frustrating for you.
Process for my machine, which should be very similar for yours:
Deploying thumb: configure stick so that it is almost parallel to the ground, bucket will be close to the cab. Bang out the retention pins. On yours, push in some 2x4 blocks or equivalent to hold the weight of the thumb somewhat while you get the pin out. Once the thumb is free, lift the boom, and push the stick out until the thumb falls on to the bucket. Once the weight of the thumb is on the bucket, curl bucket as necessary to line up the pin. On mine, the lower pin of the bar is always connected, and the upper pin is out. I would do this similarly for yours (connect lower pin first), and I would remove the bar entirely when retracting the thumb. If you are trying to line up the upper pin during this step, the weight of the bar will mostly be resting on the thumb, which will make it easier to manipulate by hand or with a small prybar.
Retracting thumb: Use the bucket to hold the weight of the thumb without applying pressure to the pins. Remove the pin from the thumb bar. On yours, I would remove the bar entirely at this step. On mine, the bar folds inside of the thumb teeth, and there is another pin point further up on the stick to hold it in place, and the lower pin where it connects to the thumb never needs to come out. I think that the ratchet strap you have shown will work in a pinch, but is very likely to break long term. After the pins are removed, fold the stick under towards the cab, and boom down, until the stick is close to parallel to the ground. From there you should be able to use the bucket to flip the thumb. This is also the part where additional tabs welded on that hit the stick would be really nice. On mine, once the thumb is tipped, the holes line up fine and you put the pins in and go on your way. On yours, you'll want to check whatever the thumb is going to hit to ensure it's rugged enough, or strap a piece of wood in place that the thumb can hit and hold it mostly at the right height. Once it's mostly folded up against the stick, you can adjust a little from there, or use a chain around the bucket to hold the weight of the thumb and maneuver it to line things up perfectly.
Once you have a process ironed out, it shouldn't be much work to flip it either direction. The key is effectively using the large machine that it's attached to. If I had to flip my thumb without using the machine, I wouldn't look forward to that task.
On another note, looking forward to following your home build. That is a very nice plan you selected, and I can't wait to see how it turns out!
