Primaries *sized* right (in other words, not too large, or too small) actually act to "suck" the incoming air/fuel charge into the cylinder during overlap. This is a big deal at all engine speeds, but as engine RPM increases, obviously the size of the primary that works best will change...you don't want backpressure, (which comes from increased intake velocity) but you don't want inefficient scavenging either.
If the primaries are too large, the exhaust pulse is affected, and instead of traveling down the pipe effectively, the pressure waves lose their direction, if you will.
Not to mention, as exhaust cools down it takes up less volume, again you start dealing with issues where the exhaust is not effectively traveling through the pipe, instead each exhaust event is "pushing" against the last one, instead of being pulled.
It's a complex subject, and very hard to get just right in application, but this is essentially how the whole "backpressure is good" argument got into peoples heads...put 2.5" primary tube headers and 4" exhaust pipes on a stock small block, compared to 1.75", and single 2.25" pipe and of course, since the exhaust isn't effective in scavenging, the smaller size does better. Some people then just assumed it was backpressure that made the smaller tubes produce more power, which is not the case.
Here is some GREAT reading, failing to read it only makes you less educated.
http://www.popularhotrodding.com/enginemasters/articles/hardcore/0505em_exh/
I just wish I had the time to try/test some of the things he mentions, like smaller exhaust in certain sections for less noise with no power penalty.
And going back to one aspect of headers and an injected engine, of course changes can be made to take advantage of the headers, more exhaust out means more air/fuel in, right? In most cases the difference between manifolds and headers can probably be compensated for by the system, but obviously changes to fueling should be made in the PROM to take FULL advantage of any modification. Anything that changes airflow, fueling, or spark requirements should be compensated for in the PROM. Doesn't have to be, but the chances that performance (dictated by the stock PROM calibration) is less than it could be are probably 99%, even on a bone stock engine.
if its a stockish small block go 2.5 if it's a Bigbbbblock or a bad ass mouse go 3"
40's might be a tad aggressive..... 
