I sure can't help anymore, BUT, did the car start normally before the flywheel and clutch replacement? If so, the work and/or parts have something to do with it.
If the DME does not get the correct signal from the crank sensor, the car will not start. There are some smart scan tools out there that can monitor the crank sensor signal. It would be prudent to check that before pulling the trans.
Ed in San Jose '97 540i 6 speed aspensilber over aubergine leather. Build date 3/97. Golden Gate Chapter BMW CCA Nr 62319.