Thanks for reporting these.
Church joining has changed a lot and compatibility between old and new versions is shaky at best.
If you loaded your old save where you already joined the church, then you should have a new "armor" in inventory called "Church talisman" or something like that (you can equip it in the "Other" slot). After that, go to the spot where the door used to be and interact with this spot:
The door should open now. If it doesn't work, try to equip / unequip the talisman. If you don't have the talisman at all and you finished the quest in the older version, then that's a mistake on my part.
As for the entrace bike bug and the shower but, I will fix these. Thanks for reporting them.