"Some time back I provided some information about accurately painting PT-109 at the time Kennedy was the boat's skipper. I've continued to do research on this subject with a variety of answers. Based on exchanging letters with Dick Keresey who was the skipper of PT-105, I'm convinced that the 109 boat was never MTB green. According to Dick, his boat was dark gray, and all the boats in his squadron (of which the 109 was a part) were gray. PT Boats Inc also states that the 109 boat was gray. There is a good picture of the 105 and 107 boats in route to Rendova with the dark gray paint scheme. So, with that in mind if you are going to paint the 109 boat after Kennedy took charge, you would paint this to match Navy spec 5D. A good match for this color is Model Masters Gunship Gray. Consider lightening up the paint with a little white to account for weathering. Take note that the Floquil naval colors are not longer being produced.
I also saw a note (above) stating that the 109 boat was called "JFK". According to Mr. Keresey his squadron didn't name their boats, or at least paint anything on them indicating their names. Photos don't show any evidence of a name painted on the 109.

Some modeling tips for the 109 under Kennedy...

1. The mast should be in the folded down position. It's possible there wasn't even a mast. All photos of the 109 boat after Kennedy took charge show no mast. Mr. Keresey said that a lot of the time the masts were left folded down, but he isn't sure about the 109.
2. Add depth charges forward of the torpedoes on each side. The 109 accidentally launched the forward port torpedo, driving the port depth charge through the deck. It was not replaced so one depth charge on the starboard side is accurate too. Consider adding a 37mm anti tank gun if you can find it. The book PT-109 describes how the gun was lashed to the deck.
3. Don't add stanchions and ropes on the foredeck. These had all been removed on all boats while in combat.
4. Don't add bow "PT-109" decals. The rest are accurate.
5. The spot light should be omitted. There is not even evidence of a mast for the spot light. The 80' Elco boats had a mounting on the port side of the cockpit. But looking at photos of the 109 cockpit with Kennedy sitting in it I noticed that the mounting point for this auxiliary mount show empty screw holes.
6. Sand off any evidence of a cockpit wind screen. The cockpit was fitted with armor plate on the front and sides. The port side of the cockpit should be the same height across and behind the wheel. Not curved as modeled. See photos for a better description."