It's not quite every puzzle, but should help.
MANSION
Piano - Combine Handkerchief and Soap and wipe the piano, avoid the Oni that will drop down and then go back and investigate. Looking at the message of the sun and moon the code it is the third number rotating while the second sits still, then the third number passes it only as its equal - only the second and third numbers are used - the third number rotates while the second is the same and then the third is used again only without rotating, then the final number would be what wasn't used.
Shrine - Use the Red Gem to get the Old Key. Take it back after.
Clock Room - The order of the red numbers are based on the dates of the deaths in order.
BASEMENT
The lighter can make hidden items shimmer when near them on the shelves in the starting room. The cage room should have its light lit and door closed, then look at the right of the door for the code to the safe.
ANNEX
Head to the attic and get the lighter fluid, then back down to the 1F and into the kitchen and use the lighter, grabbing the rotten meat from the fridge and push the dumbwaiter button to send it to the 2F. Grab the guest room key from the dumb waiter and light bulb from the lamp.
The 2F outside balcony has the code from Jeff for his room box to get powder, as well as the grams needed for the explosive. 1.25 The fireplace can be lit and the doll burned to get the Yellow Gem, and the attic will now have a number etched in you need. The doll is in the North Hall left room (Jeff's Room) and one of its eyes sparkle.
In the North Hall right side door, put the Yellow Gem into the doll there and turn off the light, then take the doll head and replace it with the lightbulb to reveal a hidden door. Back in Jeff's room, use the doll head to reveal the safe and then the code from the attic to open the safe and get the basement key.
LAB
Move the shelf to the left of the door to reveal a panel. Use the star screw driver to open it and solve the puzzle (third, first, second) to restore power. Also get the picture book on the shelf and check it for the bookmark.
Use the flathead on the door panel to undo it, then use the bookmark to figure out the door code (red, green, grey, blue)
Use vinegar on the red key from the tub room (drain the tub, push it from the top) to get the iron gate key and proceed down to the basement. Check the disc and follow its pattern to push the portraits correctly (red, yellow, yellow, blue, yellow, red) to get metal stick. Combine it with the disc to get the catacombs key.
In the catacombs grab a bunch of gun powder (you can measure it later in Jeff's room with his scales and what the note said) Combine the powder and gun powder for explosive.
OLD BUILDING (Great to explore and figure out this area on your own)
Medical Room - Push the statue and torch from the exit into the room, gold statue is left, silver right and use the flame on each side and take note of the sides of each shape.