First off use the link I gave you above as a reference for basic improvement of the kit. If you have any questions about what you see there let me know and I'll explain in detail. Much of which is written can be confusing if you don't understand the boat.
Okay, let's start at the bow and work out way to the stern of the boat.
1. Do not install the standards on the deck which hold the hand ropes. These were removable and that's exactly what the crews did. You wont see these on any of the boats in combat.
2. Do not install the the flag staff. Same thing. It is removable in real life and they were disgarded.
3. The 109 did not have a life raft on the deck. Typically these were stowed on top of the Day Cabin and sometimes the chart house. More on that later but the bottom line is that the 109 probably didn't have it's life raft when Kennedy got it.
4. The deck in general. While the early Elco boats were planked on the kit it doesn't look scale. If you have the patience consider masking off the deck detail and sanding out the wood grain effect.
5. The 109 had depth charges mounted just forward of the forward torpedo tubes. There was an accident and the port torpedo drove the port depth charge through the deck. It was repaired but at the time of the sinking the 109 had a starboard depth charge. If you need a drawing I can probably scan it and email it to you.
6. Torpedo tubes sit way to high on the kit. You can do as the author explains and remanufacture the tubes. You can also shave down the mounts a little to get it closer to scale.
7. The 109 cockpit was rebuilt. Originally the 109 had a glass windscreen. That was replaced by armor all the way around. In the article you can see on the side view of the chart house a dotted line. That's how the 109 was. To model all this sand off the detail that show the brackets for the glass all around the cockpit. Just smooth it out. Or consider getting some thin plastic sheet stock and rebuilding the whole cockpit. I'm going to give you some links that might show what I'm trying to say. It's difficult to explain. Another detail on the 109 boat is the light bracket. There was a light bracket not modeled on the kit on the port side of the cockpit. Instead of the light on the end of the pole they could mount it next to the cockpit. This is missing on the 109 boat and all that is left are the mounting holes. You could drill these holes for a nice detail that most would probably miss.
8. The windows on the front of the chart house were pained over. The windows on the side of the chart house are clear. However these boats had covers on the inside of the chart house and they were left closed most all the time. You can model this by painting and floating some future where the window would be to simulate the glass.
9. The 109 did not operate with the mast up. It is entirely possible that the mast didn't exist. I spoke with the skipper of PT-105 and he told me that it was either stowed or gone. My guess is that it was removed or lost based on similar photographs of boats not sporting the mast. Remember that the 109 was already a veteran when Kenney took command.
10. There was no radar on the 109.
11. The kit decals are all screwed up. Don't use them. The lettering on the 109 was small and there was nothing on the bow. You will find 109 markings on the front of the chart house, side of the turret, and on the mounting for the 20mm on the stern. Look at the photos and see if you can find some similar numbers as dry transfers. Maybe White Ensign Models has some ideas here.
Here are some links to PT Boat information. Check out all the links at PT Boats Inc. Also the last link here has some photos of the 109.
http://ourworld.compuserve.com/homepages/mandm/ptboatp1.htm
http://www.ptboats.org/
http://www.mysticaquarium.org/newthings/articles/pt109main.asp
Okay, that should get you going. Feel free to reach out to me anytime with any question you might have. I love these boats!
Dave