Unlike the 3er the 540i doesn't work very well with heel-&-toe technique. Firstly, the pedals are not well-located. This issue has been debated thoroughly on the ROADFLY.COM newsgroup so you can look for yourself. Most people seem to roll their ankles to the left and use the ball of their feet. But it doesn't always work. I place the heel of my foot on the brakes and point right towards the throttle with my toes. My feet are otherwise too narrow to bridge the pedals with a rolling action. All of this can be vastly improved with some modifications and new pedals. Unfortunately, there's another problem.
The other unfortunate part about the E39's design has nothing to do with the pedals. It's the electronic throttle control. This issue has also been debated on the ROADFLY.COM newsgroup. The throttle-blipping response in the 540 is severely muted because BMW chose to design the throttle to allow it to obtain a more favourable EPA gas mileage rating. Blipping the throttle in the 540i is very tricky business. It isn't predictable because it's not mechanical - the electronics decide if they should respond under a broader set of conditions, of which I have little clue to. It's better in the I-6 models as they seem less restricted by this throttle design but even they are not as responsive as older BMWs. Which E39 model do you drive?
FWIW, because I trained on a 3er I sometimes heel-&-toe instinctively in my 540i but I don't bother to do it consciously because the throttle response to blipping is so unpredictable - no sense unsettling the car when the revs don't match anyway. In any case, the torque from the V-8, post-corner, is so abundant that I can afford to take my corners a bit slower than I would have in a 3er. I just try to drive smoothly with a reserve of power in case I have to maneuver out of harm's way. I don't race on the streets.
If you want to debate what I say I would prefer to direct you to the pros and other people on ROADFLY.COM. Otherwise, it just becomes an issue of my opinion against yours. I have said all I care to on this particular topic. Here's a good webpage by pros on heel-&-toe:
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"...Heel Toe cannot be done smoothly unless two things are done:
1) The pedals must be matched. Normally this is done by adjusting until the brake and throttle are even in height, when the brakes are pressed on. The pedals must also be properly spaced. In my car it required adjusting and bending the gas pedal until I got the match I needed. In many cars, the pedals have some range of adjustment, making the process easier. One thing to remember, as you adjust the gas pedal, make sure that there is a mechanical stop for the pedal. If you rely on the stops in the carburetor or injection system to stop the motion, you will probably bend or break something as you try to squeeze a couple more horsepower out of the pedal. Also, make sure the linkage allows the butterflies in the carburetor to be fully open when the pedal hits your mechanical stop.
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