I plan on building a custom exhaust manifold for my 90 accord, but I'm not sure where to find a flange? Are there any options other than building it myself?

No, but that seems like a lot of trouble to go through when you can buy a decent header off the internet for pretty cheap. Bottom of the line ones on eBay go for $50 or you can go with OBX, Megan Racing, or DC Sports if you want to pay more. It just seems like more of a hassle than its worth. Just my 2 cents.

It sounds like an interesting idea, I'd be curious to see how much it costs you in parts given the current price of steel on a retail level.... I would suggest building the headers then remove the exhaust, cut the flange off the stock one and fit it to yours and re-weld it...