As for the Cathedral, we have a local middle and high school attached to the local Cathedral
Ah, nice, fair enough. It would be cool in the game, only currently the interior does not look the part at all. (The interior also doesn't match the outside of the church that is shown, which looks a lot more like one would expect a Cathedral too look, albeit somehow miniature.)
For the workout routine, I still kind of want to keep it because he needs to be at a "certain" level of fitness to be able to keep up with Sera and Wren on their routes or fall into laziness during the other three's routes.Oh, this sounds very cool, I thought the protagonist would never do anything questionable. :) Maybe you can just omit the hard numeric details of the morning routine, then it also feels less like bragging by the protag. (If that is not intentional - as in the confession we also wonder if the protag is not perhaps prone to bragging.)
By the way, I never read VNs, so take it all with a grain of salt.