I am going to look into my crystal ball for your engine type...but, in the mean time, I am guessing that you have a Yanmar based on your hull number and assuming it is the original engine. So you either have the 75hp or 70-"something" hp or the 100hp.
There are no "pins" on the 100hp Yanmar, originally installed by Amel on BeBe #387; and the flange on the casted stainless elbow that I bought from the eBay seller and I installed is 12mm. It installs by installing the metal gasket, then installing the elbow over threaded studs that have nuts to tighten the elbow in place.
So, since you mention "pins" and since you say the "pins" are not long enough, I must assume that either someone has modified your 100hp Yanmar, changed the original engine, OR, maybe you have the 70-"something" hp Yanmar...OR, possibly when you refer to "pins" you are referring to the threaded metal studs. If this is the case, probably someone changed those studs and did not buy the correct length.
Can you please tell me which of the above it is? And, tell me what model Yanmar and serial number you have. I suspect an engine modification or engine change is the source of your problem.
Rodney Bay Marina