I am installing new water closet in pier and beam home ,#1 can flange be mounted on top of finnished floor or does it need to be on top of sub floor ? #2 vertical drop is 13 1/2 feet from main septic line, what fitting do I need to maintain proper drop ?

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,#1 can flange be mounted on top of finnished floor or does it need to be on top of sub floor ?

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on top of the finished floor.

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#2 vertical drop is 13 1/2 feet from main septic line, what fitting do I need to maintain proper drop ?

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If I understand your question correctly you have a drop of 13.5 feet from the closet bend to the sewer main.
You will maintain 1/4" per foot and use a 1/8th bend to 45 down tom the main where it will be picked up by a upright wye that you will installe in the main. More questions? I'm as close as a click. Good luck, Tom