when using thread tape put no more than 10 turns of tape around the thread. Usually 8 will do, what ever size of fittings you are using. any more and you may split the fitting open.
As for the tape getting into the filters and pumps, that will only happen if you allow the tape to cover the opening of the fitting so when you apply the tape just put it around the thread.
As for the thread sealing paste, when you use it only apply from the middle of the thread up. As you screw on the fitting so the paste will squeeze into the thread. Only use a tiny amount. If you get it on your clothes it will not come off.