A custom tune would be better than an "off the shelf" tune for sure with or without headers but it should be ok.
2001 540i - Orient Blue
M5 bumpers, wheels, mirrors
S/C, water/air IC
A1 Headers, Random Technology Cats, Eissenmann Exhaust
3.15 diff, evosport power pullies
Koni Sports, Eibach Springs/Sway Bars