Getting 400 hp and 500 tq out of a 461 is probably just a matter of putting the thing together with whatever parts you have lying around.
If you want to be more precise than that (and why wouldn't you?) the most important thing is getting compression "right" for the fuel you have available and the head TYPE you're going to use. For iron heads, on 93 octane, shoot for 9.3:1 maybe 9.5:1 tops. In a "standard" 461 (4.155 bore, 4.25 stroke) and assuming "the usual" Pontiac piston height of about 0.015 "down", standard 0.045 (compressed) head gaskets, 92 cc's of clearance volume puts you at 9.468:1 compression. 94 cc's puts you at 9.318 compression. (Yes, just 2 cc's makes that much difference). If you're going to run aluminum heads, then your target for compression should be a full number higher - 10.3-10.5:1
The engine won't care much how you get to 92-94 cc's. You can get it from the chamber volume in the heads, you can get it from dishes in the pistons, or a combination of the two. If you go with dished pistons (and that's probably the best option since you're ordering a stroker kit anyway), make SURE you get D-shaped dishes that still have a standard height quench pad and not fully round, circular dishes. Also do NOT cheat and get that additional volume from running fat/thick head gaskets. That kills your quench properties which can actually make it more likely to get into detonation.
So, first thing: CC your heads, or have them cc'ed. You need to know exactly how much volume is in each of all 8 chambers (don't do just one) so you'll know how much dish volume you need in the pistons to bring the total to 92-94 cc's. Don't rely on factory specs for this. Pontiac heads have been known to vary from factory values enough to make a difference and besides, unless the heads have been in your possession since they were knew, who knows if they may have already been milled some in the past?
Truth be told, on a street engine I just don't think it's worth twisting the dragon's tail by trying to push compression to the limit. On a 461 like you're building, the difference between 9.3:1 and 10.3:1 (iron heads) will only amount to measly 5-8 hp, all else held equal. If you're already at 400+, is it really worth taking that chance? I don't think so, but it's your choice.
Next thing. Decide if you're going to run bolts or studs on the main caps. Either way, I recommend having the main bores at least checked for roundness and alignment and honed to get them 'perfect' if needed. The reason you want to decide that now is because if you switch from bolts to studs (or vice versa) some time in the future you'll have to have the block align honed AGAIN, and each time that operation is done, a few thousandths gets shaved off the main caps before the operation. Why does that matter? because if you have it done multiple times it can affect both the rear main seal groove (it will get further and further out of round) and also the outer shape of the rear cap where it seals to the oil pan and make it a lot harder to keep those areas from leaking. And it's hard enough already to seal the rear of a Pontiac anyway.
The goal here is to have all the machining done on the block exactly one time.
If you're handy with tools, replace the two front and driver side rear oil gallery plugs with tapped, screw in pipe plugs. Make sure to get the 'shallow' ones so that the ones in the front don't obstruct the oil passages the exit towards the inside. (The 'hidden' plug that's in front of the distributor is already a screw in pipe plug).
Get and run a good windage tray. I really like the ones that Paul Spotts makes. I'm also using his oil scraper.
Cam choice. Hoo boy that's a topic. The best advice I can give you there is to be brutally honest with yourself about how and where you're going to be driving the car 90% of the time. Those cubic inches will tend to 'tame' any cam. Even the RA IV profile which was pretty nasty in a 400, so much so that you couldn't order a IV with A/C from Pontiac, will be a lot more docile in a 461. I'm not necessarily recommending that cam (modern computer designed cam profiles are significantly better), just using it as an example of how inches affects them. Think about getting a cam that's going to place the meat of the torque curve at the RPM where you're going to be spending most of your time. I'd consider talking with the tech guys at Bullet cams and Butler to get their opinions.
If the car has power brakes, make sure the cam you choose will generate sufficient manifold vacuum to operate them - or get ready to spend money on modifying the brake system with a vacuum pump or a hydroboost system. I personally like rollers, but they're quite a bit more expensive and they also have their drawbacks. What I like about them is that you can get a lot more duration out of a roller profile without also murdering the overlap (which kills low end torque if it gets out of control), but getting quality lifters and also keeping an eye on them is of extreme importance. If one fails "in the wrong way" it can destroy the block. Something worth looking into which has come around since I built mine, is running LS roller lifters in a Pontiac. Supposedly it's not all that hard to pull off, and since you're using lifters from GM that they put in production cars that are intended these days to last multiple hundreds of thousands of miles... the idea has merit I think.
Other stuff, just don't cheap out on any of the ancillary parts, and don't let yourself get excited so that you rush and get in a hurry. That will always come back to bite you. I've got the teeth marks to prove it.
Bear
