I'm planning on using a '91 Mustang ECU on my 408W. I do plan on getting a custom chip burned for it. I have talked to several people that have run stroker motors and 351Ws in Mustangs, and the concensus is that a stock computer will work, but you won't get the full power potential of your motor without a chip or a programmer.
I plan on getting a chip from
Johnson Motorsports.
The other way to go is an EEC tuner. Downside of tuners are they are expensive and you really have to know what you're doing. Here's a couple EEC tuners sites:
Tweecer ,
EEC Tuner.com .
Pete