I abandoned the project for a few reasons:
1. The primaries on the S54 headers are so small that they did not mate up to the stainless M54 flanges that I had bought on ebay. Smaller primaries are a good thing as you don't want the collector to be a smaller cross section than the 3 primaries, but it meant I had to do what others had done and cut the mild steel flanges off of the OE exhaust manifolds and use those.
2. Getting the angles right was harder than I anticipated. I mocked them up on the car and then took the parts to work and barely tack welded the headers onto the flanges, thinking that I could bend the tack welds a bit to massage them into place on the car, then bring them back for finish welding.The fitment was too far off for that strategy. They'll need to be re-tacked in place while on the car. I don't have a welder at home and my car was stuck on the lift with no exhaust manifolds so I needed to get something on it that worked and had already chopped up my OE manifolds.
3. The transition to the rest of the exhaust was going to be a bear with changing the flange placements, and I would have to neck down from the M3 2.25" exhaust diameter to mate with our 2.0" piping. That would probably be fine for this situation, especially since you're coming straight off the cats, but you really never want to neck down in an exhaust system as it will create backpressure.
So with all that in mind and the fact that I had butchered my OE manifolds and couldn't just throw them back on, I ordered a set of 'ebay headers' on Amazon with next day shipping and got those on the car.
The results were...ok. There was a noticeable bump in power, but the ECU seemed to be chasing the fuel trims and of course my car was now catless and just cranking out poisonous gases and honda rasp. I was already this far and liked the extra torque, so I picked up some Magnaflow high flow cats and had them welded in just behind the flanges for the headers (I'll try to grab a pic the next time I'm under the car). The cats knocked down 90% of the rasp, but the cat bodies are 4" diameter, which would be great for a forced induction car, but with NA there is a big loss of exhaust gas velocity there and it sapped away most of the power that I had picked up with the headers.
So current state of my car:
Ebay headers wrapped in fiberglass shit
Magnaflow cats welded in just after the headers, beside the transmission
maybe a little more power than stock...maybe
cats take longer to heat up than OE so startups and first 5 mins of driving are noxious af, after that it's fine
I'm not thrilled with it, and would rather have stock manifolds than what is currently on the car (stock was less rasp, less emissions, same-ish power), but I'll keep working on it. I have a Borla exhaust ready to go on and may try to swap the first canister on it for a 2in-2out cat to see if it the smaller cat body keeps the velocities up.