Everything is good so far, I say so far since there wasn’t enough chaps to actually judge it good. I just wanna give ideas, don’t make the mother be a very easy capture, he is still her son, she took care of him since he was a child so there is bound to be complications when he abruptly changes his view on her, just take it slow. The big sister, perfect, couldn’t have done that better, lil sis, perfect, reminds me of ‘Little rascal doesn’t want to meet a bad end’.
Make him do exercise early on, but not to the level where after a year timeskip, he can destroy mountains, that’s stupid, just enough to get him going.
Don’t make this guy rely on his system all the time, since you wrote that he is a straight A student then he should be pretty smart, and people who are good at chess are very good at tactics and split second decision making so you can make use of that.
When he starts his first se.x scene, take advantage of the fact that he has watch a lot of **** and hentai that he knows how to pleasure women even though he is a virgin, I already tried that, and I was glad I spent a couple of hours watching po.rn and hen.tai.
Don’t let him be a pushover, It’s kinda weird being a harem protagonist while you’re being dominated in bed.
100 chaps is too long for a se.x scene, just do timeskip dude.