#1 - Remove the pieces.  The triangle cutouts are meant to relieve weight from the piece (every little bit counts), leaving that diagonal part to act as a compression strut.  There is little to be gained, except weight, by leaving those pieces in.  She'll be plenty heavy without them.  <;-)
​#2 - Install the upper mast partner doubler on the aft portion after making the cut to separate the boat.  It will overhand the joint a bit and help a little in putting the two parts together.

.....Michael

Here's a photo of that Mast Support piece affixed to the forward bulkhead and bottom before the forward seat went on:

I was wrong about the direction of the diagonal piece.  The way it slopes, it would be a tension member, not compression as I incorrectly stated above.  Kinda makes sense, now that I've thought on it.  I think the whole idea is that, as the mast presses forward under load, this piece, tied in firmly to the bottom, the bulkhead, and the underside of the forward seat, will resist flexing or buckling of the parts to which it is attached.

Anyway, you can see that the triangle shaped spaces are open.

.....Michael

I found a few pictures to show the sequence of events with that top mast partner doubler.

First, here is a shot of the boat nearly sawn in twain, showing that that piece is not yet installed:

​

Next, we see the temporarily reunited parts as we were fitting up the bolts and such, still without that upper doubler piece:

Here we are finally gluing the piece in, upside down, for all love:

​Looks like we were also working on the bottom skids at the same time.  It was October by then, so we were probably going at it hammer and tongs to get all the assembly finished before it got too cold to work with epoxy in the garage.  Nearly there.

Finally, here's the aft section ready for painting:

...plainly showing how that upper doubler piece projects over the joint between the sections.

Hope that sets your mind at rest....

.....Michael

Thank you, that was exatly what I needed, am proceeding as instructed!