Looking at those bronze bolts, I can see why they used the spacers, the threads don't go all the way down and a spacer was required. The steel plate has me puzzled, it makes little sense to do that unless you are just too lazy to cut it to size. That is most likely the case, as they appeared to be too lazy to paint it too.
I am curious about the exhaust diameter. You said it was a 3" exhaust pipe going into the muffler but smaller coming out the other side? I can see in the photo they look quite small by comparison, what size is the stock outlet for the small block? Also I am curious what diameter exhaust are you going to be using for the big block?
I saw the notes you posted about the transmissions and I think your choice of going with a Borg Warner is a good one. They make a very good product and that model (72C) is as rugged as any you will find in that power range. In case you have not already seen it, there is a good reference manual available on line here http://www.marinepartsexpress.com/bw_sch_fs.html
for these transmissions.
I'm looking forward to seeing your progress with this boat. Better get moving, springtime is only a few months away.