You could always swap a manual into it. That would solve the problem

I'm sorry to hear about all of the trouble, I'm not sure what else there is to go wrong on something like this. Does it only do this in the first to second gear shift? or is it impossible to get passed second gear?

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Running:
2001 E53 3.0i Black 5MT Style 87, Eibach Swaybars, Headers, Turner Monoball Bushings, Oil pump nut fix, E60 short shifter + ZHP shift knob, Sport Swap 204K (G-power supercharger coming soon)
2011 E70 35d Blue Style 214 3" exhaust, Dudmd stage 2, 2" HR lowering springs
2012 E70 35d Black Style 215

Sold:
2002 e39 540i 6MT Black sport, M5 LSD, M60 Intake manifold
2003 e39 525i Auto Grey Sport