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I was told that, believe it or not, tha stock chip worked better with a SC than it did with the Diablo.
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Hehe, That's funny.
Because there is no stock "chip".
There is just the ECM.
After-market chips are installed on a service port on the ECM.
Since the port is never used in most cars, the service port contacts are protected by a service port cover, protective grease and lacquer.
By changing the program on the chip and installing it on the service port, you can change the way the ECM acts and interfaces with the rest of the car.
I have no idea why a performance shop would tell you to use a stock ECM with a blower. In fact, most Mustang blower kits today REQUIRE an aftermarket chip (usually supplied) to operate normally.
One example is 99 and newer stangs with a Procharger P1SC setup.
99+ Mustangs use a "returnless" fuel system, (ie no fuel return line), so you can't use a Fuel Management Unit to increase fuel pressure when you start making boost. In order to supply enough fuel, you'll need at least 30lb injectors and an ECM module (ie "chip") in place of an FMU. This way the ECM will react correctly and provide the fuel pressure you will need.
The above is just one of the MANY things a correctly programmed chip can do for you. It also shows why a "generic" after-market chip will not yield the same results as a custom tune on modified engines.
Rush,
If you are serious about a blower, email me when you're ready to buy and I'll get you in touch with some folks down here at Dallas Mustang.
Hope this helps....