before anyone says mine are not like that -- pull your 496 fuel rail and look at the bottom sides. These pics are from the bottom side of the fuel rail and the top side looks great like brand new because Merc has paint on the top side. Bottom side like I said most have no paint and min 70 percent of the time look like this in the pics and even way worse. Just putting it out there.

the brite white you see on the fuel rail and at the seems of the injector port is aluminum oxidation as well. These fuel rails corrode badly over time

Whipple has 555pcm base cals for the HO600 kit that they tuned for previous users. IMHO you would still want to monitor A/F ratio and adjust if needed. Whipple can adjust tune if they have correct info....RPM, MAP, A/F ratio etc..

BUP is correct on the fuel rails. Mine were slightly corroded on the non painted bottom. Internally there was no corrosion though. When you install Raylar intake, the stock fuel crossover is replaced with stainless crossover and you can get to each bank rail to clean. Don't forget to send your injectors to BUP to test/clean while apart.

'04 should have the aluminum exhaust manifolds and the ports are huge in those. No scavenging though. Would work well with a blower. I know you are looking for an engine builder and maybe someone can help you on that.