I have installed an exterior (very heavy) pre-hung door manufactured for me by a local shop that is now out of business. My very new hardwood floors come up high on the threshold, leaving not enough room for an entry carpet inside the door which will cause excessive water in this area from the coming rain (Seattle). I want to cut the door shorter, and then raise the threshold with the three screws but am not sure how to figure out the correct dimensions includiing room for the rubber seal. Any thoughts for me prior to tearing into this?

Have you tried to adjust that threshold up all the way yet? I doubt that it will rise enough to meet your needs. The adjustments is usually more in fractions of an inch. To do this the way you want/need the entire door frame needs to be reset and this may require some reframing of the header.

I agree with Bob, it is doubtful that the adjustment will have that much travel. My memory says about 1/2 to 5/8" maximum. Best solution is to remove molding both sides. Cut nails through jams and move the door and frame up.

Tell us how far up you need to go. If it's just a 1/2 or so, it can be done without moving the whole door up.

I am assuming here that you want just enough clearance so that you can put a low profile matt in and open the door?

The threshold itself has to be looked at. Take a picture so we can take a look. The threshold and door.