A 429 will run in a jet boat but between a 429 and a 460 I'll take the 460 almost every time, especially if you have an A impeller.
The main issue with the 429 is that there is only one set of forged shelf pistons available for them, the TRW/Speed-Pro L2366. Those pistons and D3's put you at about 8.75:1 c/r, and C9's will put you at about 10.5:1 c/r. They also weigh 1000+ grams with the pin.
If you switch to a 460 crankshaft (uses your same rods) you will have dozens of pistons options in dish, flat top, dome, etc. A 460 crank is the cheapest "+31 cubic inch stroker crank" out there for you, and you can run compression ratios pretty much wherever you want, from 8.5:1 to 13:1 with readily available shelf pistons. And 450hp is a walk in the park with these engines.
I have to agree that taking apart a good running engine is not always the greatest idea. Perhaps it might be better to keep it as a spare and build another longblock and can transfer the bolt-ons (pan, induction, distributor, exh, etc) between the two. Sounds like you already have some C9 heads. I have blocks cranks rods, heads, etc, stock, modified, if you want anything. Feel free to call.
LO
p.s.: If you want more power out of your current engine, you might swap the D3VE's out for the C9VE's (if that's your current combo). There is more to this than just the swap (valve train) but if you are considering it I'll get into greater detail.