I own a couple of SCX rally cars, and both went really well when new - A few mods as youve described should sort out most cars, but it sounds like you have a mechanical, rather than as setup fault.
Could be a couple of things....
1) front axle bent.. was my first thought..
2) trued the front tyres or the rear tyres too much and made them smaller.
Front tyres to small... rears driving hard down the straight, apply brakes, front axle makes contact with the track surface, gianing grip, and as they are smaller, they have a difrent rotatoinal speed to the rear. They are trying to gain grip... (ok the brakes are applied but they dont stop instantly, they still rotate for a while - 6 inches is enough)....
Either ensure that the front and rear tyre diameters are pretty much the same, or glaze the fronts.
Slight dissadvantage is you loose the pull on acceleration of 4 wheel drive.
Hope that helps