The tranny isn't an issue. I know of guys running 500+ HP and twist the propshaft off without putting a dent in the tranny. I'm running 400HP on my bone stock OEM tranny with 1400 hrs. on it. Never been rebuilt but has had the seals and gaskets replaced. As long as you change your fluid like your supposed to, it'll be fine.
If you want more holeshot, leave the engine alone and put an Acme 541 prop on it. You'll be amazed at the performance improvement. That by itself should probably be sufficient for your needs.
GT40P heads and a Stealth or Performer RPM intake will indeed give you another 40+HP. Probably the best bang for your buck performance increase you'll ever find. Don't mess with junk yard Explorer heads either. Call Tristate or Clearwater heads. Pick up a set completely worked over with new valves, guides and ready to install for about $600/pr. Just make sure that you tell them you want brass freeze plugs and to drill out the head bolt holes to accept 1/2" bolts. You're good to go.
That along with the 541 Acme is a really hot ticket.
My bigger concern is your WOT top speed. 40 sounds a little slow to me. What boat, how many hours and when was the last time a tune up was done on it?