Being worried is normal, OniBan. I also am while wanting only the best for Shoma as well.
To alleviate your worries a bit, Lombardia was the first time Shoma did his Free Skate with competition layout under the new rules. All those quads and combos in a 4 minutes Free Skate takes a lot out of all the male skaters, including Shoma, especially because Shoma has a 4-quad layout. As the season moves forward, I think Shoma has improved his stamina to deal with it, you can see him in Skate Canada (full steam at the start but running out of gas at the end), and in NHK and GPF he seems to have distributed his power more evenly.
And of course at Nationals, Shoma have told us that he did pull/sprain his ankle in one of the warm-up practices before SP, which have attributed to the pop at the axel and his performances.
As for uncharacteristic mistakes at the GP series... I do love Shoma, but there are days when he doesn't go clean, and it happens.
I am also worried with the new schedule (to be fair I worry about Shoma almost all the time.. I'm like this with my favorites). At the same time, I think Shoma also wants more ice and competition time especially after the long rest after nationals? If he's been focusing on recovery, that means less ice and practice time for him, and historically he's a skater who have used minor competitions to improve and get more confidence in his programs. The rest between 4CC and Worlds is quite long, it makes sense that Shoma would want the competition in between. The good thing is after Challenge Cup, Shoma will be fully Japan-bound even if he gets assigned to WTT and this season, he has had good results in Japan.
Plus, Shoma has Demi-san on his side

Having a personal trainer doesn't guarantee you'll be injury-free, but having someone like Demi-san with him assures me that Shoma is also looking out for his longetivity. I still worry, but I try to believe in him