I dove the site again and managed to note the markings on the side and solve the mystery of the pin.
Each boat has a number; 203 and 91.
Both boats also have the following same markings:
2E/EO 1210
Folding Boat Mk3
4 ESD
Jan 55
RCSME
I figure Jan 55 is the manufacture date and RCSME stands for Royal Canadian School of Military Engineering. I think 4ESD is 4 Engineer Supply Depot. Still working on 2E/Eo 1210.
The pin mystery is solved. It holds the load bearing girders in place on the boat gunnel superstructure. I saw one in place on the boats. They were not connected by a leather tether as I first suspected but rather by small link chain.
I also found this anchor next to the wreckage but don't know if it was part of the boats or just an unrelated snag.
On Thursday I'm diving with a DIR team that is interested in doing a site survey as they have just finished taking an UW archeology course and are keen to put their learning into practice. I still plan to research the history via military records and some contacts I've made but I'll probably turn the wreckage over to them and get back to studying fish.