To prevent any future confusion I decided it would be best to make this post before I get ahead of myself.
Shuichi is presented as a very feminine boy, and is often mistaken for a girl unless his clothing is very specifically male (such as his school uniform). While Shuichi is physically a boy he often presents himself as female, wearing a wig and female clothes. He is completely convincing as a female (and in fact very cute, which can cause its own trouble!) and really only those who are fairly familiar with him would recognize him with his wig.
To reduce confusion for the muns interacting with him I've decided that I will switch pronoun sets based on the situation at hand. If Shu is presenting as a boy he will be referred to as such, and if he is presenting as a girl 'he' will be referred to as 'she'. However if the muse interacting with him is aware of his situation then I will probably choose to refer to him as a boy.
If anyone thinks there is a better way to go about this then do speak up as I'd be willing to hear and take it into consideration!
Secondly I'd like to use this post to briefly mention Shu's gender identity. Although in both the Wandering Son manga and anime he is presented as a boy evidence heavily suggests that Shu is not simply a crossdresser but a transwoman, meaning that he has the mind of a girl but the body of a boy. Shu frequently expresses his (or 'her', as would be more appropriate but I won't go into that here) desire to be female and often has dreams relating to his gender identity.
There's some debate within the fandom as to whether this was the authors intention or not and whether Shu is indeed trans but evidence within the manga (there is evidence present in the anime but it's harder to interpret and the anime generally gives off a mixed message (in my opinion at least)) heavily suggests that Shu is indeed trans even if the mangaka has not yet outright stated it. So call it head-canon if you will but this is the reading that I'll be following through with.
I'll happily answer any questions here, but if they're more generally related to Shu's personality outside of his genderbending please use the HMD post.