Greetings,
Let's start with references. The best books out there outside of the one identified already are..
United States PT-Boats of World War II by Frank D. Johnson
American PT Boats in World War II by Victor Chun
Allied Coastal Forces of World War II, Volume II by John Lambert & Al Ross (my favorite for details)
I would also suggest going to http://www.ptboat.org/ web site and check out the forum there. You can also buy reference material from them. It just requires some time to research.
As far as parts for upgrading the kits go...
The White Ensign Models (WEM) photoetch set has some nice parts to it but a lot of it IMHO is worthless. I bought this set and used parts of it to make masters for some resin castings I made. (Not for sale John, only my own personal use! :-) )
For the later model boats you can find some nice upgrades at WEM including the 40mm, 37mm, and roll off torpedoes. Also check out Nautilus Models who has some resin castings of some guns in 1/72 scale.
John Haynes in England has a very nice 20mm Oerlikon that works well for the 103 class boats including your earlier boat identified.
Really it depends on what period you model the boat. I don't think any two boats were identical in configuration and paint. The crews did whatever they could to give them an advantage.
Here are some photos of my 109 boat prior to paint that show some of the changes I made to this model. Note the last photo shows the John Haynes 20mm pedestal in place of the kit molding.