Originally Posted by speedball1
"Should this connect to the stench pipe or the extractor fan?"
NO!! They should be exhausted outside.
"Will the stench pipe breath normally now i have removed all the board and installation from around it and stop the smell?"
Not if it's capped off. Leaving it capped will prevent the fixture traps from venting once you drain the fixture. The capped vent should be run out the roof or revented back into the main roof vent. You do have a vent running out the roof don't you? regards, Tom