Mike,
I have 3 of the Dumas PT boats and you're absolutely right about the amount of work it's going to take you as there is a lot of building that is needed if you go strictly per the instructions
As for the drive shafts my first model had three screws but I ended up not using the center screw as the power to weight was just not worth it.
All of my PT boats were powered using only two screws with Graupner 12V Speed 700BB motors and twin MCD speed controllers. With this setup the speeds are awesome and I run with a 12V gel cell battery which is a little heavier than a nicad pack but I can get more that double the run time.
Two of my hulls use a modified shaft assembly which consists of a strut and a shorter stuffing box. This is more to scale bit you need to make sure that you do the alignment between the struts the shafts and the stuffing boxs otherwise you get some binding which will cause drag and a reduction in speed and run time. My first boats running gear was done per the Dumas plans and i was not too happy with the way it looked.
I went the expensive route and build my second and third hulls using some aftermarket fittings that you can get from such places as Mosquito Boat Hobbies, HR Products. I've purchased several fitting packages from Mosquito Boat Hobbies and am very happy with the quality and service. One word of caution is these pieces can be expensive. My last fittings kit was around $400 and was a Christmas gift from my wife in 2002. Boy was I surprised!
If you're a stickler for scale the Dumas kit has several small problems that are not to scale on their hulls. To correct this you need to rework the bow which is initially a little scary but definite well worth the fitting of the deck to the hull.

As for your rudders I found that the scale rudders did not give me the control that I needed so I over sized them slightly but still kept te same shape. This made a world of difference in being able to maneuver the boat at slower speeds. To help I have a Nautical Commander Ace radio with twin throttle sticks with twin speed controllers which allows me to operate each motor independently. I can pivot this boat in its own length.
Let me know if you want any more information.
Tom