Yeah, the Ram Air 3 D-port manifolds will bolt up to most D-port heads.
The easiest way to make 400hp is to put a 4.25 stroker assembly, into your 400 block(most any 400 block except those with a casting number ending in 557). Butler sells a balanced cast crank assembly for about $1600 or a little more shipped.
Butler Performance - Pontiac Engine & Rotating Assembly Combinations - Featuring Eagle Pontiac Kits
If you have a few hundred more to spend on the shortblock, you can get the stroker assembly with a forged crank, H-beam rods, and even Ross pistons. And by going with a forged crank, you can also go with a 4.21" 455 stroke, and Pontiac length 6.625 rods.
With this stroker shortblock you can use the 6x heads, and RA3 manifolds. The RA3 mainifolds are not quite as good as open headers. But, if you're gonna run a full exhaust system, the manifolds will be almost as good as headers.
There are several sources for the RA3 manifolds. RARE is one source. They are not cheap. Painted headers are much cheaper.
Pontiac Ram Air Manifolds
Max/Pypes also sell the manifolds.
" Are there any viable options for running Ram Air heads on a stock 400?..."
The round port RA heads cost too much. The D-port RA heads are cheaper, but still cost more than the 6x heads. Plus, they give a 400 too much compression for pump gas, unless you run dish pistons. So, for the price of the RA heads and dish pistons, you might as well add just a little more to it and go with a stroker and 6x heads. IMO