Hey Guy,
I am doing the same conversion on mine, (once I get done with a massive nose job... she needs a boob job too so....). Anyway let's compare notes.
My plan is to replace the decks too, but it looks like you don't need to do that.
I am going to try to keep the two fish boxes, and extend a step/platform between them. I had a mako172 angler, which had a rear platform, which was great to fish from (I fly fish and light tackle mostly). If you don't try to keep the two fishboxes, it will probably be a little easier. I am not planning to do a cap across the top of the transom, but if you remove the fish boxes, you might want to think about it. I think that is what strick and others have done on theirs.
My first cut was going to be in front of the fish boxes (1 in photo), from the topcap, across the gunnel, down to the deck. Then across the deck (2) and around the motor well (3). Then smaller cuts to remove the topcap from the transom. At this point I was going to remove those two fish boxes carefully, but if you aren't going to keep them then just rip them out. I was planning to keep the top of the gunnels.